Get started
851 commits | Last commit ≈ 25 months ago
Ctrl K
MAGMa
MAGMa is an online application for the automatic chemical annotation of mass spectrometry data.
95
mentions
3
contributors
Cite this software
What MAGMa can do for you
- Supports mass spectrometrists to chemically annotate fragmentation data
- Retrieves and ranks candidate molecules and substructures for parent and product ions
- Provides metabolic reaction rules to generate candidate molecules
- Provides a powerful user interface to interpret the results
Keywords
Programming languages
License
</>Source code
Participating organisations
Reference papers
Journal articles
2- 1.Author(s): Lars RidderPublished in Current Metabolomics by Bentham Science Publishers Ltd. in 2017, page: 18-2410.2174/2213235x04666160620100844
- 2.Author(s): Lars Ridder, Justin J. J. van der Hooft, Stefan VerhoevenPublished in Mass Spectrometry by The Mass Spectrometry Society of Japan in 2014, page: S0033-S003310.5702/massspectrometry.s0033
Mentions
Book section
4- 1.Author(s): Milinda A. Samaraweera, Dennis W. Hill, David F. GrantPublished in Methods in Molecular Biology, Ion Mobility-Mass Spectrometry by Springer US in 2019, page: 283-29510.1007/978-1-0716-0030-6_18
- 2.Author(s): Timothy M.D. Ebbels, Jake T.M. Pearce, Noureddin Sadawi, Jianliang Gao, Robert C. GlenPublished in The Handbook of Metabolic Phenotyping by Elsevier in 2019, page: 329-36710.1016/b978-0-12-812293-8.00011-6
- 3.Author(s): Joanna Godzien, Alberto Gil de la Fuente, Abraham Otero, Coral BarbasPublished in Comprehensive Analytical Chemistry, Data Analysis for Omic Sciences: Methods and Applications by Elsevier in 2018, page: 415-44510.1016/bs.coac.2018.07.004
- 4.Author(s): Velitchka V. Mihaleva, Fatma Yelda Ünlü, Jacques Vervoort, Lars RidderPublished in Molecular and Integrative Toxicology, Metabonomics and Gut Microbiota in Nutrition and Disease by Springer London in 2014, page: 109-12410.1007/978-1-4471-6539-2_6
Journal articles
73- 1.Author(s): B. L. Milman, I. K. ZhurkovichPublished in Journal of Analytical Chemistry by Pleiades Publishing Ltd in 2024, page: 119-13310.1134/s1061934824020126
- 2.Author(s): Jun Xue, Bingyi Wang, Hongchao Ji, WeiHua LiPublished in Bioinformatics by Oxford University Press (OUP) in 202410.1093/bioinformatics/btae084
- 3.Author(s): Б. Л. Мильман, И. К. ЖурковичPublished in Журнал аналитической химии by The Russian Academy of Sciences in 202410.31857/s0044450224020029
- 4.Author(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.Author(s): Michael A. StravsPublished in CHIMIA by Swiss Chemical Society in 2024, page: 525-53010.2533/chimia.2024.525
- 6.Author(s): Elva María Novoa-del-Toro, Michael WittingPublished in Metabolomics by Springer Science and Business Media LLC in 202410.1007/s11306-024-02167-2
- 7.Author(s): Janne Heirman, Wout BittremieuxPublished in Nature Machine Intelligence by Springer Science and Business Media LLC in 202410.1038/s42256-024-00909-4
- 8.Author(s): Scarlet Ferrinho, Helen Connaris, Nigel J. Mouncey, Rebecca J.M. GossPublished in Water Research by Elsevier BV in 2024, page: 12149210.1016/j.watres.2024.121492
- 9.Author(s): Jun Zeng, Yaping Li, Chuanlin Wang, Sheng Fu, Min HePublished in Talanta by Elsevier BV in 2024, page: 12551410.1016/j.talanta.2023.125514
- 10.Author(s): Haotian Wang, Laijin Zhong, Wenyuan Su, Ting Ruan, Guibin JiangPublished in TrAC Trends in Analytical Chemistry by Elsevier BV in 2024, page: 11798810.1016/j.trac.2024.117988
- 11.Author(s): Peter Tarábek, Nataliia Leonova, Olga Konovalova, Michal KirchnerPublished in Chemosphere by Elsevier BV in 2024, page: 14348910.1016/j.chemosphere.2024.143489
- 12.Author(s): Otun Sarah, Achilonu Ikechukwu, Ntushelo KhayalethuPublished in Journal of Plant Science and Phytopathology by Heighten Science Publications Corporation in 2023, page: 027-03810.29328/journal.jpsp.1001102
- 13.Author(s): Gurpur Rakesh D. Prabhu, Evan R. Williams, Matthias Wilm, Pawel L. UrbanPublished in Nature Reviews Methods Primers by Springer Science and Business Media LLC in 202310.1038/s43586-023-00203-4
- 14.Author(s): Erandika Karunaratne, Dennis W. Hill, Kai Dührkop, Sebastian Böcker, David F. GrantPublished in Analytical Chemistry by American Chemical Society (ACS) in 2023, page: 11901-1190710.1021/acs.analchem.3c00937
- 15.Author(s): Yaping Xu, Jie Li, Huajian Mao, Wei You, Jia Chen, Hua Xu, Jianfeng Wu, Ying Gong, Lei Guo, Tao Liu, Wuju Li, Bin Xu, Jianwei XiePublished in Food and Chemical Toxicology by Elsevier BV in 2023, page: 11373810.1016/j.fct.2023.113738
- 16.Author(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
- 17.Author(s): Fei Wang, Daniel Pasin, Michael A. Skinnider, Jaanus Liigand, Jan-Niklas Kleis, David Brown, Eponine Oler, Tanvir Sajed, Vasuk Gautam, Stephen Harrison, Russell Greiner, Leonard J. Foster, Petur Weihe Dalsgaard, David S. WishartPublished in Analytical Chemistry by American Chemical Society (ACS) in 2023, page: 18326-1833410.1021/acs.analchem.3c02413
- 18.Author(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
- 19.Author(s): Michael J. Taylor, Hoshin Kim, William Kew, Amity Andersen, Arunima Bhattacharjee, Mark H. Engelhard, Christopher R. AndertonPublished in Biointerphases by American Vacuum Society in 202310.1116/6.0002298
- 20.Author(s): Shuangqian Shen, Chuansong Zhan, Chenkun Yang, Alisdair R. Fernie, Jie LuoPublished in Molecular Plant by Elsevier BV in 2023, page: 43-6310.1016/j.molp.2022.09.007
- 21.Author(s): Nikiforos Alygizakis, Francois Lestremau, Pablo Gago-Ferrero, Rubén Gil-Solsona, Katarzyna Arturi, Juliane Hollender, Emma L. Schymanski, Valeria Dulio, Jaroslav Slobodnik, Nikolaos S. ThomaidisPublished in TrAC Trends in Analytical Chemistry by Elsevier BV in 2023, page: 11694410.1016/j.trac.2023.116944
- 22.Author(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
- 23.Author(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
- 24.Author(s): Shijuan Yan, Ruchika Bhawal, Zhibin Yin, Theodore W. Thannhauser, Sheng ZhangPublished in Molecular Horticulture by Springer Science and Business Media LLC in 202210.1186/s43897-022-00038-9
- 25.Author(s): Fei Wang, Jaanus Liigand, Siyang Tian, David Arndt, Russell Greiner, David S. WishartPublished in Analytical Chemistry by American Chemical Society (ACS) in 2021, page: 11692-1170010.1021/acs.analchem.1c01465
- 26.Author(s): Hiroshi Tsugawa, Amit Rai, Kazuki Saito, Ryo NakabayashiPublished in Natural Product Reports by Royal Society of Chemistry (RSC) in 2021, page: 1729-175910.1039/d1np00014d
- 27.Author(s): Christine M. Fisher, Timothy R. Croley, Ann M. KnolhoffPublished in TrAC Trends in Analytical Chemistry by Elsevier BV in 2021, page: 11618810.1016/j.trac.2021.116188
- 28.Author(s): Erandika Karunaratne, Dennis W. Hill, Philipp Pracht, José A. Gascón, Stefan Grimme, David F. GrantPublished in Analytical Chemistry by American Chemical Society (ACS) in 2021, page: 10688-1069610.1021/acs.analchem.1c02244
- 29.Author(s): Aditya Divyakant Shrivastava, Neil Swainston, Soumitra Samanta, Ivayla Roberts, Marina Wright Muelas, Douglas B. KellPublished in Biomolecules by MDPI AG in 2021, page: 179310.3390/biom11121793
- 30.Author(s): Sophie Alvarez, Michael J. NaldrettPublished in Emerging Topics in Life Sciences by Portland Press Ltd. in 2021, page: 189-20110.1042/etls20200271
- 31.Author(s): Anis Irfan Norazhar, Soo Yee Lee, Siti Munirah Mohd Faudzi, Khozirah ShaariPublished in Applied Sciences by MDPI AG in 2021, page: 352610.3390/app11083526
- 32.Author(s): Fidele Ntie-Kang, Kiran K. Telukunta, Serge A. T. Fobofou, Victor Chukwudi Osamor, Samuel A. Egieyeh, Marilia Valli, Yannick Djoumbou-Feunang, Maria Sorokina, Conrad Stork, Neann Mathai, Paul Zierep, Ana L. Chávez-Hernández, Miquel Duran-Frigola, Smith B. Babiaka, Romuald Tematio Fouedjou, Donatus B. Eni, Simeon Akame, Augustine B. Arreyetta-Bawak, Oyere T. Ebob, Jonathan A. Metuge, Boris D. Bekono, Mustafa A. Isa, Raphael Onuku, Daniel M. Shadrack, Thommas M. Musyoka, Vaishali M. Patil, Justin J. J. van der Hooft, Vanderlan da Silva Bolzani, José L. Medina-Franco, Johannes Kirchmair, Tilmann Weber, Özlem Tastan Bishop, Marnix H. Medema, Ludger A. Wessjohann, Jutta Ludwig-MüllerPublished in Journal of Cheminformatics by Springer Science and Business Media LLC in 202110.1186/s13321-021-00546-8
- 33.Author(s): Marcus Ludwig, Corey D. Broeckling, Pieter C. Dorrestein, Kai Dührkop, Emma L. Schymanski, Sebastian Böcker, Louis-Félix NothiasPublished in Journal of the American Society for Mass Spectrometry by American Chemical Society (ACS) in 2020, page: 180-18610.1021/jasms.0c00240
- 34.Author(s): Zeqin Guo, Sheng Huang, Jianhua Wang, Yong-Lai FengPublished in Talanta by Elsevier BV in 2020, page: 12133910.1016/j.talanta.2020.121339
- 35.Author(s): Partho Sen, Santosh Lamichhane, Vivek B Mathema, Aidan McGlinchey, Alex M Dickens, Sakda Khoomrung, Matej OrešičPublished in Briefings in Bioinformatics by Oxford University Press (OUP) in 2020, page: 1531-154210.1093/bib/bbaa204
- 36.Author(s): Sean M. Colby, Dennis G. Thomas, Jamie R. Nuñez, Douglas J. Baxter, Kurt R. Glaesemann, Joseph M. Brown, Meg A. Pirrung, Niranjan Govind, Justin G. Teeguarden, Thomas O. Metz, Ryan S. RenslowPublished in Analytical Chemistry by American Chemical Society (ACS) in 2019, page: 4346-435610.1021/acs.analchem.8b04567
- 37.Author(s): Biswapriya B. MisraPublished in Current Pollution Reports by Springer Science and Business Media LLC in 2019, page: 93-11110.1007/s40726-019-00109-4
- 38.Author(s): Myungjae Kwak, Kyungwoo Kang, Yingfeng WangPublished in Journal of Computer Information Systems by Informa UK Limited in 2019, page: 12-1810.1080/08874417.2019.1681328
- 39.Author(s): Christoph Ruttkies, Steffen Neumann, Stefan PoschPublished in BMC Bioinformatics by Springer Science and Business Media LLC in 201910.1186/s12859-019-2954-7
- 40.Author(s): Aurélien F. A. Moumbock, Fidele Ntie-Kang, Sergi H. Akone, Jianyu Li, Mingjie Gao, Kiran K. Telukunta, Stefan GüntherPublished in Physical Sciences Reviews by Walter de Gruyter GmbH in 201910.1515/psr-2018-0126
- 41.Author(s): Hongchao Ji, Yamei Xu, Hongmei Lu, Zhimin ZhangPublished in Analytical Chemistry by American Chemical Society (ACS) in 2019, page: 5629-563710.1021/acs.analchem.8b05405
- 42.Author(s): Ivana Blaženović, Tobias Kind, Jian Ji, Oliver FiehnPublished in Metabolites by MDPI AG in 2018, page: 3110.3390/metabo8020031
- 43.Author(s): Yuichi Miyake, Masahiro Tokumura, Qi Wang, Takashi Amagai, Yasuhiro Takegawa, Yoko Yamagishi, Sayaka Ogo, Kazunari Kume, Takeshi Kobayashi, Shinji Takasu, Kumiko Ogawa, Kurunthachalam KannanPublished in Environmental Science & Technology Letters by American Chemical Society (ACS) in 2018, page: 448-45510.1021/acs.estlett.8b00263
- 44.Author(s): Jean-Luc Wolfender, Jean-Marc Nuzillard, Justin J. J. van der Hooft, Jean-Hugues Renault, Samuel BertrandPublished in Analytical Chemistry by American Chemical Society (ACS) in 2018, page: 704-74210.1021/acs.analchem.8b05112
- 45.Author(s): Florbela Pereira, Joao Aires-de-SousaPublished in Marine Drugs by MDPI AG in 2018, page: 23610.3390/md16070236
- 46.Author(s): Hiroshi TsugawaPublished in Current Opinion in Biotechnology by Elsevier BV in 2018, page: 10-1710.1016/j.copbio.2018.01.008
- 47.Author(s): Ricardo R. da Silva, Mingxun Wang, Louis-Félix Nothias, Justin J. J. van der Hooft, Andrés Mauricio Caraballo-Rodríguez, Evan Fox, Marcy J. Balunas, Jonathan L. Klassen, Norberto Peporine Lopes, Pieter C. DorresteinPublished in PLOS Computational Biology by Public Library of Science (PLoS) in 2018, page: e100608910.1371/journal.pcbi.1006089
- 48.Author(s): Milinda A. Samaraweera, L. Mark Hall, Dennis W. Hill, David F. GrantPublished in Analytical Chemistry by American Chemical Society (ACS) in 2018, page: 12752-1276010.1021/acs.analchem.8b03118
- 49.Author(s): Liang Cui, Haitao Lu, Yie Hou LeePublished in Mass Spectrometry Reviews by Wiley in 2018, page: 772-79210.1002/mas.21562
- 50.Author(s): Alberto Gil de la Fuente, Emily Grace Armitage, Abraham Otero, Coral Barbas, Joanna GodzienPublished in ELECTROPHORESIS by Wiley in 2017, page: 2242-225610.1002/elps.201700070
Presentations
3- 1.Published in 2014
- 2.Published in 2012
- 3.Published in 2012
Video recordings
1Webpages
1Other
12- 1.Author(s): Janne Heirman, Wout BittremieuxPublished by American Chemical Society (ACS) in 202410.26434/chemrxiv-2024-97r5j
- 2.Author(s): Thomas O. Metz, Christine H. Chang, Vasuk Gautam, Afia Anjum, Siyang Tian, Fei Wang, Sean M. Colby, Jamie R. Nunez, Madison R. Blumer, Arthur S. Edison, Oliver Fiehn, Dean P. Jones, Shuzhao Li, Edward T. Morgan, Gary J. Patti, Dylan H. Ross, Madelyn R. Shapiro, Antony J. Williams, David S. WishartPublished by Cold Spring Harbor Laboratory in 202410.1101/2024.07.30.605945
- 3.Author(s): Peter Tarábek, Nataliia Leonova, Olga Konovalova, Michal KirchnerPublished by Elsevier BV in 202410.2139/ssrn.4860575
- 4.Author(s): Umit Volkan Ucak, Islambek Ashyrmamatov, Juyong LeePublished by American Chemical Society (ACS) in 202410.26434/chemrxiv-2024-vrqzf
- 5.Author(s): Umit Volkan Ucak, Islambek Ashyrmamatov, Juyong LeePublished by American Chemical Society (ACS) in 202410.26434/chemrxiv-2024-vrqzf-v2
- 6.Author(s): jun xue, Bingyi Wang, Weihua liPublished by American Chemical Society (ACS) in 202310.26434/chemrxiv-2023-pf268
- 7.Author(s): jun xue, Bingyi Wang, Weihua liPublished by American Chemical Society (ACS) in 202310.26434/chemrxiv-2023-pf268-v2
- 8.Author(s): Aditya Divyakant Shrivastava, Neil Swainston, Soumitra Samanta, Ivayla Roberts, Marina Wright Muelas, Douglas Bruce KellPublished by MDPI AG in 202110.20944/preprints202110.0355.v1
- 9.Author(s): Mehmet Aziz Yirik, Kumsal Ecem Colpan, Saskia Schmidt, Maria Sorokina, Christoph SteinbeckPublished by MDPI AG in 202110.20944/preprints202111.0546.v1
- 10.Author(s): Adamo Young, Bo Wang, Hannes RöstPublished in 2021
- 11.Author(s): Aditya Divyakant Shrivastava, Neil Swainston, Soumitra Samanta, Ivayla Roberts, Marina Wright Muelas, Douglas B. KellPublished by Cold Spring Harbor Laboratory in 202110.1101/2021.06.25.449969
- 12.Author(s): Marcus Ludwig, Corey D. Broeckling, Pieter Dorrestein, Kai Dührkop, Emma Schymanski, Sebastian Boecker, Louis-Felix NothiasPublished by American Chemical Society (ACS) in 202010.26434/chemrxiv.12114987.v1
Testimonials
My group has had an excellent run of almost 1 year now running MAGMa as part of our cluster-based compound ID workflow - it is really a great program.
– Lee Ferguson, Department of Civil & Environmental Engineering, Duke University
Contributors
Contact person
Lars Ridder
Netherlands eScience Center
MS
Marijn Sanders
Netherlands eScience Center
Netherlands eScience Center
Related projects
Chemical Informatics for Metabolite Identification and Biochemical Network Reconstruction
Chemical informatics for metabolite identification and biochemical network reconstruction
Updated 20 months ago
Finished