The Sirius API wrapper for LC-BinBase
Build the docker image or pull it from ECR, and then run
- docker run -p 80:80 --name sirius <image-name>
Kai Dührkop, Markus Fleischauer, Marcus Ludwig, Alexander A. Aksenov, Alexey V. Melnik, Marvin Meusel, Pieter C. Dorrestein, Juho Rousu and Sebastian Böcker. SIRIUS 4: Turning tandem mass spectra into metabolite structure information. Nature Methods 16, 299–302, 2019.
Michael A. Stravs and Kai Dührkop, Sebastian Böcker and Nicola Zamboni. MSNovelist: De novo structure generation from mass spectra. Nature Methods 19, 865–870, 2022. (Cite if you are using: MSNovelist)
Martin A. Hoffmann, Louis-Félix Nothias, Marcus Ludwig, Markus Fleischauer, Emily C. Gentry, Michael Witting, Pieter C. Dorrestein, Kai Dührkop and Sebastian Böcker. High-confidence structural annotation of metabolites absent from spectral libraries. Nature Biotechnology 40, 411–421, 2022. (Cite if you are using: CSI:FingerID, COSMIC)
Kai Dührkop, Louis-Félix Nothias, Markus Fleischauer, Raphael Reher, Marcus Ludwig, Martin A. Hoffmann, Daniel Petras, William H. Gerwick, Juho Rousu, Pieter C. Dorrestein and Sebastian Böcker. Systematic classification of unknown metabolites using high-resolution fragmentation mass spectra. Nature Biotechnology, 2021. (Cite if you are using CANOPUS)
Yannick Djoumbou Feunang, Roman Eisner, Craig Knox, Leonid Chepelev, Janna Hastings, Gareth Owen, Eoin Fahy, Christoph Steinbeck, Shankar Subramanian, Evan Bolton, Russell Greiner, David S. Wishart. ClassyFire: automated chemical classification with a comprehensive, computable taxonomy. Journal of Cheminformatics 8, 61, 2016. (ClassyFire publication; cite this if you are using CANOPUS)
Marcus Ludwig, Louis-Félix Nothias, Kai Dührkop, Irina Koester, Markus Fleischauer, Martin A. Hoffmann, Daniel Petras, Fernando Vargas, Mustafa Morsy, Lihini Aluwihare, Pieter C. Dorrestein, Sebastian Böcker. Database-independent molecular formula annotation using Gibbs sampling through ZODIAC. Nature Machine Intelligence 2, 629–641, 2020. (Cite if you are using ZODIAC)
Kai Dührkop and Sebastian Böcker. Fragmentation trees reloaded. Journal of Cheminformatics 8, 5, 2016. (Cite this for fragmentation pattern analysis and fragmentation tree computation)
Kai Dührkop, Huibin Shen, Marvin Meusel, Juho Rousu, and Sebastian Böcker. Searching molecular structure databases with tandem mass spectra using CSI:FingerID. Proceedings of the National Academy of Sciences U S A 112(41), 12580-12585, 2015. (cite this when using CSI:FingerID)
Sebastian Böcker, Matthias C. Letzel, Zsuzsanna Lipták and Anton Pervukhin. SIRIUS: decomposing isotope patterns for metabolite identification. Bioinformatics 25(2), 218-224, 2009. (Cite this for isotope pattern analysis)
Shipei Xing, Sam Shen, Banghua Xu, Xiaoxiao Li and Tao Huan. BUDDY: molecular formula discovery via bottom-up MS/MS interrogation. Nature Methods 20, 881–890, 2023. (Cite if you are using: Bottom-up molecular formula generation)
Marcus Ludwig, Kai Dührkop and Sebastian and Böcker. Bayesian networks for mass spectrometric metabolite identification via molecular fingerprints. Bioinformatics, 34(13): i333-i340. 2018. Proc. of Intelligent Systems for Molecular Biology (ISMB 2018). (Cite for CSI:FingerID Scoring)
W. Timothy J. White, Stephan Beyer, Kai Dührkop, Markus Chimani and Sebastian Böcker. Speedy Colorful Subtrees. In Proc. of Computing and Combinatorics Conference (COCOON 2015), volume 9198 of Lect Notes Comput Sci, pages 310-322. Springer, Berlin, 2015. (cite this on why computations are swift, even on a laptop computer)
Huibin Shen, Kai Dührkop, Sebastian Böcker and Juho Rousu. Metabolite Identification through Multiple Kernel Learning on Fragmentation Trees. Bioinformatics, 30(12):i157-i164, 2014. Proc. of Intelligent Systems for Molecular Biology (ISMB 2014). (Introduces the machinery behind CSI:FingerID)
Imran Rauf, Florian Rasche, François Nicolas and Sebastian Böcker. Finding Maximum Colorful Subtrees in practice. J Comput Biol, 20(4):1-11, 2013. (More, earlier work on why computations are swift today)
Heinonen, M.; Shen, H.; Zamboni, N.; Rousu, J. Metabolite identification and molecular fingerprint prediction through machine learning. Bioinformatics, 2012. Vol. 28, nro 18, pp. 2333-2341. (Introduces the idea of predicting molecular fingerprints from tandem MS data)
Florian Rasche, Aleš Svatoš, Ravi Kumar Maddula, Christoph Böttcher, and Sebastian Böcker. Computing Fragmentation Trees from Tandem Mass Spectrometry Data. Analytical Chemistry (2011) 83 (4): 1243–1251. (Cite this for introduction of fragmentation trees as used by SIRIUS)
Sebastian Böcker and Florian Rasche. Towards de novo identification of metabolites by analyzing tandem mass spectra. Bioinformatics (2008) 24 (16): i49-i55. (The very first paper to mention fragmentation trees as used by SIRIUS)