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Detecting and quantifying products of cellular metabolism using Mass Spectrometry (MS) has already shown great promise in many biological and biomedical applications.
A functional genomics strategy that uses metabolome data to reveal the phenotype of silent mutations
L. M. Raamsdonk, B. Teusink, D. Broadhurst, N. Zhang, A. Hayes, M. C. Walsh, J. A. Berden, K. M. Brindle, D. B. Kell, J. J. Rowland, H. V. Westerhoff, K. van Dam, and S. G. Oliver · 2001
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Metabolomics – the link between genotypes and phenotypes
Oliver Fiehn · 2002
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METLIN: A Metabolite Mass Spectral Database
Colin A Smith, Grace O?? Maille, Elizabeth J Want, Chuan Qin, Sunia A Trauger, Theodore R Brandon, Darlene E Custodio, Ruben Abagyan, and Gary Siuzdak · 2005
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HMDB: The Human Metabolome Database
David S. Wishart, Dan Tzur, Craig Knox, Roman Eisner, An Chi Guo, Nelson Young, Dean Cheng, Kevin Jewell, David Arndt, Summit Sawhney, Chris Fung, Lisa Nikolai, Mike Lewis, Marie-Aude Coutouly, Ian Forsythe, Peter Tang, Savita Shrivastava, Kevin Jeroncic, Paul Stothard, Godwin Amegbey, David Block, David D. Hau, James Wagner, Jessica Miniaci, Melisa Clements, Mulu Gebremedhin, Natalie Guo, Ying Zhang, Gavin E. Duggan, Glen D. MacInnis, Alim M. Weljie, Reza Dowlatabadi, Fiona Bamforth, Derrick Clive, Russ Greiner, Liang Li, Tom Marrie, Brian D. Sykes, Hans J. Vogel, and Lori Querengesser · 2007
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Development and validation of a spectral library searching method for peptide identification from MS/MS
Henry Lam, Eric W. Deutsch, James S. Eddes, Jimmy K. Eng, Nichole King, Stephen E. Stein, and Ruedi Aebersold · 2007
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FiD: A software for ab initio structural identification of product ions from tandem mass spectrometric data
Markus Heinonen, Ari Rantanen, Taneli Mielikäinen, Juha Kokkonen, Jari Kiuru, Raimo A. Ketola, and Juho Rousu · 2008
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https://onlinelibrary.wiley.com/doi/full/10.1002/jms.1777
MassBank: A public repository for sharing mass spectral data for life sciences - Horai - 2010 - Journal of Mass Spectrometry - Wiley Online Library · 2010
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In silico fragmentation for computer assisted identification of metabolite mass spectra
Sebastian Wolf, Stephan Schmidt, Matthias Müller-Hannemann, and Steffen Neumann · 2010
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Rectified linear units improve restricted boltzmann machines
Vinod Nair and Geoffrey E. Hinton · 2010
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Metagenomic biomarker discovery and explanation
Nicola Segata, Jacques Izard, Levi Waldron, Dirk Gevers, Larisa Miropolsky, Wendy S. Garrett, and Curtis Huttenhower · 2011
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Computing fragmentation trees from tandem mass spectrometry data
Florian Rasche, Ales Svatos, Ravi Kumar Maddula, Christoph Böttcher, and Sebastian Böcker · 2011
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Metabolomics: The apogee of the omics trilogy
Gary J. Patti, Oscar Yanes, and Gary Siuzdak · 2012
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New Advances in Separation Science for Metabolomics: Resolving Chemical Diversity in a Post-Genomic Era
Naomi L. Kuehnbaum and Philip Britz-McKibbin · 2013
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A novel stable isotope labelling assisted workflow for improved untargeted LC–HRMS based metabolomics research
Christoph Bueschl, Bernhard Kluger, Marc Lemmens, Gerhard Adam, Gerlinde Wiesenberger, Valentina Maschietto, Adriano Marocco, Joseph Strauss, Stephan Bödi, Gerhard G. Thallinger, Rudolf Krska, and Rainer Schuhmacher · 2014
Cited alongside, same era.
HAMMER: Automated operation of mass frontier to construct in silico mass spectral fragmentation libraries
Jiarui Zhou, Ralf J. M. Weber, J. William Allwood, Robert Mistrik, Zexuan Zhu, Zhen Ji, Siping Chen, Warwick B. Dunn, Shan He, and Mark R. Viant · 2014
Searching molecular structure databases with tandem mass spectra using CSI:FingerID
Kai Dührkop, Huibin Shen, Marvin Meusel, Juho Rousu, and Sebastian Böcker · 2015
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Neural Message Passing for Quantum Chemistry
Justin Gilmer, Samuel S. Schoenholz, Patrick F. Riley, Oriol Vinyals, and George E. Dahl · 2017
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Semi-Supervised Classification with Graph Convolutional Networks
Thomas N. Kipf and Max Welling · 2017
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Gated Graph Sequence Neural Networks
Yujia Li, Daniel Tarlow, Marc Brockschmidt, and Richard Zemel · 2017
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Cited alongside, same era.
Fragment Formula Calculator (FFC): Determination of Chemical Formulas for Fragment Ions in Mass Spectrometric Data
André Wegner, Daniel Weindl, Christian Jäger, Sean C. Sapcariu, Xiangyi Dong, Gregory Stephanopoulos, and Karsten Hiller · 2014
Cited alongside, same era.
CFM-ID: A web server for annotation, spectrum prediction and metabolite identification from tandem mass spectra
Felicity Allen, Allison Pon, Michael Wilson, Russ Greiner, and David Wishart · 2014
Cited alongside, same era.
Metabolite identification through multiple kernel learning on fragmentation trees
Huibin Shen, Kai Dührkop, Sebastian Böcker, and Juho Rousu · 2014
Cited alongside, same era.
Analytical Methods in Untargeted Metabolomics: State of the Art in 2015
Arnald Alonso, Sara Marsal, and Antonio Julià · 2015
Cited alongside, same era.
Competitive fragmentation modeling of ESI-MS/MS spectra for putative metabolite identification
Felicity Allen, Russ Greiner, and David Wishart · 2015
Cited alongside, same era.
https://www.acdlabs.com/products/adh/ms/ms_frag/
Accurately Predict Mass Spec Fragmentation | ACD/MS Fragmenter
Cited in the paper.
Yann N. Dauphin, Angela Fan, Michael Auli, and David Grangier · 2017
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Adam: A Method for Stochastic Optimization
Diederik P. Kingma and Jimmy Ba · 2017
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Petar Veličkovi¢, Guillem Cucurull, Arantxa Casanova, Adriana Romero, Pietro Liò, and Yoshua Bengio · 2018
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Rapid Prediction of Electron–Ionization Mass Spectrometry Using Neural Networks
Jennifer N. Wei, David Belanger, Ryan P. Adams, and D. Sculley · 2019
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A Comprehensive Survey on Graph Neural Networks
Zonghan Wu, Shirui Pan, Fengwen Chen, Guodong Long, Chengqi Zhang, and Philip S. Yu · 2020
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