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MS2Mol: A transformer model for illuminating dark chemical space from mass spectra

Thomas Butler, Abraham Frandsen, Rose Lightheart, Brian Bargh, Thomas Kerby, Kiana West, Joseph Davison, James Taylor, Christoph Krettler, TJ Bollerman, Gennady Voronov, Kevin Moon, Tobias Kind, Pieter Dorrestein, August Allen, Viswa Colluru, David Healey

Version 4 posted 06 September 2023

3,728

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2

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Analytical Chemistry

Working Paper

Reproducible mass spectrometry data processing and compound annotation in MZmine 3

Tito Damiani, Steffen Heuckeroth, Aleksandr Smirnov, Olena Mokshyna, Corinna Brungs, Ansgar Korf, Joshua Smith, Paolo Stincone, Nicola Dreolin, Louis-Félix Nothias, Tuulia Hyötyläinen, Matej Orešič, Uwe Karst, Pieter Dorrestein, Daniel Petras, Xiuxia Du, Justin van der Hooft, Robin Schmid, Tomáš Pluskal

Version 2 posted 11 March 2024

5,630

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Analytical Chemistry

Working Paper

Efficient generation of open multi-stage fragmentation mass spectral libraries

Corinna Brungs, Robin Schmid, Steffen Heuckeroth, Aninda Mazumdar, Matúš Drexler, Pavel Šácha, Pieter C. Dorrestein, Daniel Petras, Louis-Felix Nothias, Václav Veverka, Radim Nencka, Zdeněk Kameník, Tomáš Pluskal

Version 2 posted 10 October 2024

1,222

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Analytical Chemistry

Working Paper

Enabling pan-repository reanalysis for big data science of public metabolomics data

Yasin El Abiead, Michael Strobel, Thomas Payne, Eoin Fahy, Claire O’Donovan, Shankar Subramamiam, Juan Antonio Vizcaino, Simone Zuffa, Shipei Xing, Helena Mannochio-Russo, Ipsita Mohanty, Haoqi Nina Zhao, Andres Mauricio Caraballo-Rodriguez, Paulo Wender Portal Gomes, Nicole Elizabeth Avalon, Pieter C Dorrestein, Mingxun Wang

Version 1 posted 16 April 2024

642

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1

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Analytical Chemistry

Working Paper

Reproducible Molecular Networking Of Untargeted Mass Spectrometry Data Using GNPS.

Allegra T. Aron, Emily Gentry, Kerry L. McPhail, Louis Felix Nothias, Mélissa Nothias-Esposito, Amina Bouslimani, Daniel Petras, Julia M. Gauglitz, Nicole Sikora, Fernando Vargas, Justin J. J. van der Hooft, Madeleine Ernst, Kyo Bin Kang, Christine M. Aceves, Andrés Mauricio Caraballo-Rodríguez, Irina Koester, Kelly C. Weldon, Samuel BERTRAND, Catherine Roullier, Kunyang Sun, Richard M. Tehan, Cristopher A. Boya, Christian Martin H., Marcelino Gutiérrez, Aldo Moreno Ulloa, Javier Andres Tejeda Mora, Randy Mojica-Flores, Johant Lakey-Beitia, Victor Vásquez-Chaves, Angela I. Calderón, Nicole Tayler, Robert A. Keyzers, Fidele Tugizimana, Nombuso Ndlovu, Alexander A. Aksenov, Alan K. Jarmusch, Robin Schmid, Andrew W. Truman, Nuno Bandeira, Mingxun Wang, Pieter Dorrestein

Version 1 posted 08 August 2019

3,898

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5

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Earth, Space, and Environmental Chemistry

Working Paper

Non-targeted tandem mass spectrometry enables the visualization of organic matter chemotype shifts in coastal seawater

Daniel Petras, Jeremiah J. Minich, Lucia B. Cancelada, Ralph R. Torres, Emily Kunselman, Mingxun Wang, Margot E. White, Eric E. Allen, Kimberley A. Prather, Lihini I. Aluwihare, Pieter C. Dorrestein

Version 3 posted 14 October 2020

1,749

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Analytical Chemistry

Working Paper

Mining the NIST Mass Spectral Library Reveals the Extent of Sodium Assisted Inductive Cleavage in Collision-Induced Fragmentation

Marcus Ludwig, Corey D. Broeckling, Pieter Dorrestein, Kai Dührkop, Emma Schymanski, Sebastian Boecker, Louis-Felix Nothias

Version 1 posted 13 April 2020

580

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1

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Organic Chemistry

Working Paper

Monomeric and Dimeric Bromophenols from the Red Alga Ceramium Sp. with Antioxidant and Anti-Inflammatory Activities

Yi Zhang, Evgenia Glukhov, Haobin Yu, Lena Gerwick, Pieter Dorrestein, William Gerwick

Version 1 posted 05 August 2020

375

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Earth, Space, and Environmental Chemistry

Working Paper

Mass difference matching unfolds hidden molecular structures of dissolved organic matter

Carsten Simon, Kai Dührkop, Daniel Petras, Vanessa-Nina Roth, Sebastian Böcker, Pieter Dorrestein, Gerd Gleixner

Version 3 posted 06 June 2022

734

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Analytical Chemistry

Working Paper

The molecular effect of wearing silver-threaded clothing on the human skin

Alexey Melnik, Chris Callewaert, Kathleen Dorrestein, Rosie Broadhead, Jeremiah J. Minich, Madeleine Ernst, Greg Humphrey, Gail Ackermann, Rob Gathercole, Alexander A. Aksenov, Rob Knight, Pieter C. Dorrestein

Version 1 posted 08 September 2022

467

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1

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18 results in Pieter Dorrestein in Authors: Pieter Dorrestein

MS2Mol: A transformer model for illuminating dark chemical space from mass spectra

Reproducible mass spectrometry data processing and compound annotation in MZmine 3

Efficient generation of open multi-stage fragmentation mass spectral libraries

Enabling pan-repository reanalysis for big data science of public metabolomics data

Reproducible Molecular Networking Of Untargeted Mass Spectrometry Data Using GNPS.

Non-targeted tandem mass spectrometry enables the visualization of organic matter chemotype shifts in coastal seawater

Mining the NIST Mass Spectral Library Reveals the Extent of Sodium Assisted Inductive Cleavage in Collision-Induced Fragmentation

Monomeric and Dimeric Bromophenols from the Red Alga Ceramium Sp. with Antioxidant and Anti-Inflammatory Activities

Mass difference matching unfolds hidden molecular structures of dissolved organic matter

The molecular effect of wearing silver-threaded clothing on the human skin

18 results in Authors: Pieter Dorrestein