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Highly Accurate Chemical Formula Prediction Tool Utilizing High-Resolution Mass Spectra, MS/MS Fragmentation, Heuristic Rules, and Isotope Pattern Matching
Pluskal, Tomáš, Uehara, Taisuke, Yanagida, Mitsuhiro
Published in Analytical chemistry (Washington) (15.05.2012)
Published in Analytical chemistry (Washington) (15.05.2012)
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Journal Article
PBS3 and EPS1 Complete Salicylic Acid Biosynthesis from Isochorismate in Arabidopsis
Torrens-Spence, Michael P., Bobokalonova, Anastassia, Carballo, Valentina, Glinkerman, Christopher M., Pluskal, Tomáš, Shen, Amber, Weng, Jing-Ke
Published in Molecular plant (02.12.2019)
Published in Molecular plant (02.12.2019)
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Journal Article
The chloroalkaloid (−)-acutumine is biosynthesized via a Fe(II)- and 2-oxoglutarate-dependent halogenase in Menispermaceae plants
Kim, Colin Y., Mitchell, Andrew J., Glinkerman, Christopher M., Li, Fu-Shuang, Pluskal, Tomáš, Weng, Jing-Ke
Published in Nature communications (20.04.2020)
Published in Nature communications (20.04.2020)
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Journal Article
A Red Algal Bourbonane Sesquiterpene Synthase Defined by Microgram-Scale NMR-Coupled Crystalline Sponge X‑ray Diffraction Analysis
Kersten, Roland D, Lee, Shoukou, Fujita, Daishi, Pluskal, Tomáš, Kram, Susan, Smith, Jennifer E, Iwai, Takahiro, Noel, Joseph P, Fujita, Makoto, Weng, Jing-Ke
Published in Journal of the American Chemical Society (22.11.2017)
Published in Journal of the American Chemical Society (22.11.2017)
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Journal Article
Contribution of Untargeted Metabolomics for Future Assessment of Biotech Crops
Christ, Bastien, Pluskal, Tomáš, Aubry, Sylvain, Weng, Jing-Ke
Published in Trends in plant science (01.12.2018)
Published in Trends in plant science (01.12.2018)
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Journal Article
Integrative analysis of multimodal mass spectrometry data in MZmine 3
Schmid, Robin, Heuckeroth, Steffen, Korf, Ansgar, Smirnov, Aleksandr, Myers, Owen, Dyrlund, Thomas S., Bushuiev, Roman, Murray, Kevin J., Hoffmann, Nils, Lu, Miaoshan, Sarvepalli, Abinesh, Zhang, Zheng, Fleischauer, Markus, Dührkop, Kai, Wesner, Mark, Hoogstra, Shawn J., Rudt, Edward, Mokshyna, Olena, Brungs, Corinna, Ponomarov, Kirill, Mutabdžija, Lana, Damiani, Tito, Pudney, Chris J., Earll, Mark, Helmer, Patrick O., Fallon, Timothy R., Schulze, Tobias, Rivas-Ubach, Albert, Bilbao, Aivett, Richter, Henning, Nothias, Louis-Félix, Wang, Mingxun, Orešič, Matej, Weng, Jing-Ke, Böcker, Sebastian, Jeibmann, Astrid, Hayen, Heiko, Karst, Uwe, Dorrestein, Pieter C., Petras, Daniel, Du, Xiuxia, Pluskal, Tomáš
Published in Nature biotechnology (01.04.2023)
Published in Nature biotechnology (01.04.2023)
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Journal Article
The Chemistry Development Kit (CDK) v2.0: atom typing, depiction, molecular formulas, and substructure searching
Willighagen, Egon L., Mayfield, John W., Alvarsson, Jonathan, Berg, Arvid, Carlsson, Lars, Jeliazkova, Nina, Kuhn, Stefan, Pluskal, Tomáš, Rojas-Chertó, Miquel, Spjuth, Ola, Torrance, Gilleain, Evelo, Chris T., Guha, Rajarshi, Steinbeck, Christoph
Published in Journal of cheminformatics (06.06.2017)
Published in Journal of cheminformatics (06.06.2017)
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Journal Article
Rapid MALDI-MS/MS-Based Profiling of Lipid A Species from Gram-Negative Bacteria Utilizing Trapped Ion Mobility Spectrometry and mzmine
Rudt, Edward, Froning, Matti, Heuckeroth, Steffen, Ortmann, Lucas, Diemand, Julia, Hörnschemeyer, Linus, Pleger, Alexander, Vinzelberg, Max, Schmid, Robin, Pluskal, Tomáš, Dobrindt, Ulrich, Hayen, Heiko, Korf, Ansgar
Published in Analytical chemistry (Washington) (15.04.2025)
Published in Analytical chemistry (Washington) (15.04.2025)
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Journal Article
Guiding the choice of informatics software and tools for lipidomics research applications
Ni, Zhixu, Wölk, Michele, Jukes, Geoff, Mendivelso Espinosa, Karla, Ahrends, Robert, Aimo, Lucila, Alvarez-Jarreta, Jorge, Andrews, Simon, Andrews, Robert, Bridge, Alan, Clair, Geremy C., Conroy, Matthew J., Fahy, Eoin, Gaud, Caroline, Goracci, Laura, Hartler, Jürgen, Hoffmann, Nils, Kopczyinki, Dominik, Korf, Ansgar, Lopez-Clavijo, Andrea F., Malik, Adnan, Ackerman, Jacobo Miranda, Molenaar, Martijn R., O’Donovan, Claire, Pluskal, Tomáš, Shevchenko, Andrej, Slenter, Denise, Siuzdak, Gary, Kutmon, Martina, Tsugawa, Hiroshi, Willighagen, Egon L., Xia, Jianguo, O’Donnell, Valerie B., Fedorova, Maria
Published in Nature methods (01.02.2023)
Published in Nature methods (01.02.2023)
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Journal Article
Ion identity molecular networking for mass spectrometry-based metabolomics in the GNPS environment
Schmid, Robin, Petras, Daniel, Nothias, Louis-Félix, Wang, Mingxun, Aron, Allegra T., Jagels, Annika, Tsugawa, Hiroshi, Rainer, Johannes, Garcia-Aloy, Mar, Dührkop, Kai, Korf, Ansgar, Pluskal, Tomáš, Kameník, Zdeněk, Jarmusch, Alan K., Caraballo-Rodríguez, Andrés Mauricio, Weldon, Kelly C., Nothias-Esposito, Melissa, Aksenov, Alexander A., Bauermeister, Anelize, Albarracin Orio, Andrea, Grundmann, Carlismari O., Vargas, Fernando, Koester, Irina, Gauglitz, Julia M., Gentry, Emily C., Hövelmann, Yannick, Kalinina, Svetlana A., Pendergraft, Matthew A., Panitchpakdi, Morgan, Tehan, Richard, Le Gouellec, Audrey, Aleti, Gajender, Mannochio Russo, Helena, Arndt, Birgit, Hübner, Florian, Hayen, Heiko, Zhi, Hui, Raffatellu, Manuela, Prather, Kimberly A., Aluwihare, Lihini I., Böcker, Sebastian, McPhail, Kerry L., Humpf, Hans-Ulrich, Karst, Uwe, Dorrestein, Pieter C.
Published in Nature communications (22.06.2021)
Published in Nature communications (22.06.2021)
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Journal Article
Software and Computational Tools for LC-MS-Based Epilipidomics: Challenges and Solutions
Damiani, Tito, Bonciarelli, Stefano, Thallinger, Gerhard G., Koehler, Nikolai, Krettler, Christoph A., Salihoğlu, Arif K., Korf, Ansgar, Pauling, Josch K., Pluskal, Tomáš, Ni, Zhixu, Goracci, Laura
Published in Analytical chemistry (Washington) (10.01.2023)
Published in Analytical chemistry (Washington) (10.01.2023)
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Journal Article
An evaluation methodology for machine learning-based tandem mass spectra similarity prediction
Strobel, Michael, Gil-de-la-Fuente, Alberto, Zare Shahneh, Mohammad Reza, Abiead, Yasin El, Bushuiev, Roman, Bushuiev, Anton, Pluskal, Tomáš, Wang, Mingxun
Published in BMC bioinformatics (11.07.2025)
Published in BMC bioinformatics (11.07.2025)
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Journal Article
The Reference Genome Sequence of Scutellaria baicalensis Provides Insights into the Evolution of Wogonin Biosynthesis
Zhao, Qing, Yang, Jun, Cui, Meng-Ying, Liu, Jie, Fang, Yumin, Yan, Mengxiao, Qiu, Wenqing, Shang, Huiwen, Xu, Zhicheng, Yidiresi, Reheman, Weng, Jing-Ke, Pluskal, Tomáš, Vigouroux, Marielle, Steuernagel, Burkhard, Wei, Yukun, Yang, Lei, Hu, Yonghong, Chen, Xiao-Ya, Martin, Cathie
Published in Molecular plant (01.07.2019)
Published in Molecular plant (01.07.2019)
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Journal Article
Reproducible mass spectrometry data processing and compound annotation in MZmine 3
Heuckeroth, Steffen, Damiani, Tito, Smirnov, Aleksandr, Mokshyna, Olena, Brungs, Corinna, Korf, Ansgar, Smith, Joshua David, Stincone, Paolo, Dreolin, Nicola, Nothias, Louis-Félix, Hyötyläinen, Tuulia, Orešič, Matej, Karst, Uwe, Dorrestein, Pieter C., Petras, Daniel, Du, Xiuxia, van der Hooft, Justin J. J., Schmid, Robin, Pluskal, Tomáš
Published in Nature protocols (01.09.2024)
Published in Nature protocols (01.09.2024)
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Journal Article