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MAGMa
MAGMa is an online application for the automatic chemical annotation of mass spectrometry data.
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mentions
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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
- Apache-2.0
</>Source code
Participating organisations
Reference papers
Journal articles
2- 1.MAGMa-Based Mass Spectrum Annotation in CASMI 2014Author(s): Lars RidderPublished in Current Metabolomics by Bentham Science Publishers Ltd. in 2017, page: 18-2410.2174/2213235X04666160620100844
- 2.Automatic Compound Annotation from Mass Spectrometry Data Using MAGMaAuthor(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.Big Data and Databases for Metabolic PhenotypingAuthor(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
- 2.MolFind2: A Protocol for Acquiring and Integrating MS3 Data to Improve In Silico Chemical Structure Elucidation for MetabolomicsAuthor(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
- 3.Metabolite Annotation and IdentificationAuthor(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.Automated Annotation of Microbial and Human Flavonoid-Derived MetabolitesAuthor(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
67- 1.RT-Transformer: Retention time prediction for metabolite annotation to assist in metabolite identificationAuthor(s): Jun Xue, Bingyi Wang, Hongchao Ji, WeiHua LiPublished in 202410.1093/bioinformatics/btae084
- 2.New Trends in Chemical Identification MethodologyAuthor(s): B. L. Milman, I. K. ZhurkovichPublished in Journal of Analytical Chemistry by Pleiades Publishing Ltd in 2024, page: 119-13310.1134/s1061934824020126
- 3.Compendium of Metabolomic and Genomic Datasets for Cyanobacteria: Mined the GapAuthor(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
- 4.Combination of in silico prediction and convolutional neural network framework for targeted screening of metabolites from LC-HRMS fingerprints: A case study of “Pericarpium Citri Reticulatae - Fructus Aurantii”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
- 5.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
- 6.Metabolomics-centered mining of plant metabolic diversity and function: Past decade and future perspectivesAuthor(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
- 7.The secondary metabolites profiling of the phytopathogenic fungus Sclerotinia SclerotiorumAuthor(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
- 8.Deep Learning-Enabled MS/MS Spectrum Prediction Facilitates Automated Identification Of Novel Psychoactive SubstancesAuthor(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
- 9.Mass spectrometry using electrospray ionizationAuthor(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
- 10.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
- 11.Combining Experimental with Computational Infrared and Mass Spectra for High-Throughput Nontargeted Chemical Structure IdentificationAuthor(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
- 12.Atomistic simulations for investigation of substrate effects on lipid in-source fragmentation in secondary ion mass spectrometryAuthor(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
- 13.Towards a harmonized identification scoring system in LC-HRMS/MS based non-target screening (NTS) of emerging contaminantsAuthor(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
- 14.Structural annotation, semi-quantification and toxicity prediction of pyrrolizidine alkaloids from functional food: In silico and molecular networking strategyAuthor(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
- 15.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
- 16.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
- 17.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
- 18.Recent advances in proteomics and metabolomics in plantsAuthor(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
- 19.CFM-ID 4.0: More Accurate ESI-MS/MS Spectral Prediction and Compound IdentificationAuthor(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
- 20.Data processing strategies for non-targeted analysis of foods using liquid chromatography/high-resolution mass spectrometryAuthor(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
- 21.Metabolomics and complementary techniques to investigate the plant phytochemical cosmosAuthor(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
- 22.Computational Applications in Secondary Metabolite Discovery (CAiSMD): an online workshopAuthor(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
- 23.Mass spectrometry based untargeted metabolomics for plant systems biologyAuthor(s): Sophie Alvarez, Michael J. NaldrettPublished in Emerging Topics in Life Sciences by Portland Press Ltd. in 2021, page: 189-20110.1042/etls20200271
- 24.MassGenie: A Transformer-Based Deep Learning Method for Identifying Small Molecules from Their Mass SpectraAuthor(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
- 25.Metabolite Profiling of Christia vespertilionis Leaf Metabolome via Molecular Network ApproachAuthor(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
- 26.High-Throughput Non-targeted Chemical Structure Identification Using Gas-Phase Infrared SpectraAuthor(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
- 27.Studying Charge Migration Fragmentation of Sodiated Precursor Ions in Collision-Induced Dissociation at the Library ScaleAuthor(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
- 28.Recent advances in non-targeted screening analysis using liquid chromatography - high resolution mass spectrometry to explore new biomarkers for human exposureAuthor(s): Zeqin Guo, Sheng Huang, Jianhua Wang, Yong-Lai FengPublished in Talanta by Elsevier BV in 2020, page: 12133910.1016/j.talanta.2020.121339
- 29.Deep learning meets metabolomics: a methodological perspectiveAuthor(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
- 30.ISiCLE: A Quantum Chemistry Pipeline for Establishing in Silico Collision Cross Section LibrariesAuthor(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
- 31.Deep MS/MS-Aided Structural-Similarity Scoring for Unknown Metabolite IdentificationAuthor(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
- 32.Methods of Metabolite Identification Using MS/MS DataAuthor(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
- 33.An overview of tools, software, and methods for natural product fragment and mass spectral analysisAuthor(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
- 34.Metabolomics Tools to Study Links Between Pollution and Human Health: an Exposomics PerspectiveAuthor(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
- 35.Improving MetFrag with statistical learning of fragment annotationsAuthor(s): Christoph Ruttkies, Steffen Neumann, Stefan PoschPublished in BMC Bioinformatics by Springer Science and Business Media LLC in 201910.1186/s12859-019-2954-7
- 36.Evaluation of an Artificial Neural Network Retention Index Model for Chemical Structure Identification in Nontargeted MetabolomicsAuthor(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
- 37.Accelerating Metabolite Identification in Natural Product Research: Toward an Ideal Combination of Liquid Chromatography–High-Resolution Tandem Mass Spectrometry and NMR Profiling, <i>in Silico</i> Databases, and ChemometricsAuthor(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
- 38.Advances in computational metabolomics and databases deepen the understanding of metabolismsAuthor(s): Hiroshi TsugawaPublished in Current Opinion in Biotechnology by Elsevier BV in 2018, page: 10-1710.1016/j.copbio.2018.01.008
- 39.Identification of Novel Phosphorus-Based Flame Retardants in Curtains Purchased in Japan Using Orbitrap Mass SpectrometryAuthor(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
- 40.Propagating annotations of molecular networks using in silico fragmentationAuthor(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
- 41.Challenges and emergent solutions for LC‐MS/MS based untargeted metabolomics in diseasesAuthor(s): Liang Cui, Haitao Lu, Yie Hou LeePublished in Mass Spectrometry Reviews by Wiley in 2018, page: 772-79210.1002/mas.21562
- 42.Software Tools and Approaches for Compound Identification of LC-MS/MS Data in MetabolomicsAuthor(s): Ivana Blaženović, Tobias Kind, Jian Ji, Oliver FiehnPublished in Metabolites by MDPI AG in 2018, page: 3110.3390/metabo8020031
- 43.Computational Methodologies in the Exploration of Marine Natural Product LeadsAuthor(s): Florbela Pereira, Joao Aires-de-SousaPublished in Marine Drugs by MDPI AG in 2018, page: 23610.3390/md16070236
- 44.Identification of small molecules using accurate mass MS/MS searchAuthor(s): Tobias Kind, Hiroshi Tsugawa, Tomas Cajka, Yan Ma, Zijuan Lai, Sajjan S. Mehta, Gert Wohlgemuth, Dinesh Kumar Barupal, Megan R. Showalter, Masanori Arita, Oliver FiehnPublished in Mass Spectrometry Reviews by Wiley in 2017, page: 513-53210.1002/mas.21535
- 45.MAGMa-Based Mass Spectrum Annotation in CASMI 2014Author(s): Lars RidderPublished in Current Metabolomics by Bentham Science Publishers Ltd. in 2017, page: 18-2410.2174/2213235X04666160620100844
- 46.MIDAS-G: a computational platform for investigating fragmentation rules of tandem mass spectrometry in metabolomicsAuthor(s): Yingfeng Wang, Xutao Wang, Xiaoqin ZengPublished in Metabolomics by Springer Science and Business Media LLC in 201710.1007/s11306-017-1258-z
- 47.From chromatogram to analyte to metabolite. How to pick horses for courses from the massive web resources for mass spectral plant metabolomicsAuthor(s): Leonardo Perez de Souza, Thomas Naake, Takayuki Tohge, Alisdair R FerniePublished in GigaScience by Oxford University Press (OUP) in 201710.1093/gigascience/gix037
- 48.Integrating tools for non-targeted analysis research and chemical safety evaluations at the US EPAAuthor(s): Jon R. Sobus, John F. Wambaugh, Kristin K. Isaacs, Antony J. Williams, Andrew D. McEachran, Ann M. Richard, Christopher M. Grulke, Elin M. Ulrich, Julia E. Rager, Mark J. Strynar, Seth R. NewtonPublished in Journal of Exposure Science & Environmental Epidemiology by Springer Science and Business Media LLC in 2017, page: 411-42610.1038/s41370-017-0012-y
- 49.Comprehensive comparison of in silico MS/MS fragmentation tools of the CASMI contest: database boosting is needed to achieve 93% accuracyAuthor(s): Ivana Blaženović, Tobias Kind, Hrvoje Torbašinović, Slobodan Obrenović, Sajjan S. Mehta, Hiroshi Tsugawa, Tobias Wermuth, Nicolas Schauer, Martina Jahn, Rebekka Biedendieck, Dieter Jahn, Oliver FiehnPublished in Journal of Cheminformatics by Springer Science and Business Media LLC in 201710.1186/s13321-017-0219-x
- 50.CASMI 2016: A manual approach for dereplication of natural products using tandem mass spectrometryAuthor(s): Dejan NikolićPublished in Phytochemistry Letters by Elsevier BV in 2017, page: 292-29610.1016/j.phytol.2017.01.006
Presentations
3- 1.Computer assisted identification of green tea metabolites in human urinePublished in 2014
- 2.MAGMa, metabolite identification at the interface between metabolomics and chemoinformaticsPublished in 2012
- 3.Netherlands Metabolomics Centre symposiumPublished in 2012
Video recordings
1Other
5- 1.Review on Chemical Graph Theory and Its Application in Computer-Assisted Structure ElucidationAuthor(s): Mehmet Aziz Yirik, Kumsal Ecem Colpan, Saskia Schmidt, Maria Sorokina, Christoph SteinbeckPublished by MDPI AG in 202110.20944/preprints202111.0546.v1
- 2.MassFormer: Tandem Mass Spectrum Prediction with Graph Transformers.Author(s): Adamo Young, Bo Wang, Hannes RöstPublished in 2021
- 3.MassGenie: a transformer-based deep learning method for identifying small molecules from their mass spectraAuthor(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
- 4.Mining the NIST Mass Spectral Library Reveals the Extent of Sodium Assisted Inductive Cleavage in Collision-Induced FragmentationAuthor(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
- 5.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
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
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Updated 12 months ago
Finished