Proceedings of the EuBIC-MS developers meeting 2023

Pedro Beltrao; Tim Van Den Bossche; Ralf Gabriels; Tanja Holstein; Tobias Kockmann; Alireza Nameni; Christian Panse; Ralph Schlapbach; Ludwig Lautenbacher; Matthias Mattanovich; Alexey Nesvizhskii; Bart Van Puyvelde; Jonas Scheid; Veit Schwämmle; Maximilian Strauss; Anna Klimovskaia Susmelj; Matthew The; Henry Webel; Mathias Wilhelm; Dirk Winkelhardt; Witold E. Wolski; Muyao Xi

doi:10.1016/j.jprot.2024.105246

Proceedings of the EuBIC-MS developers meeting 2023

Pedro Beltrao, Tim Van Den Bossche, Ralf Gabriels, Tanja Holstein, Tobias Kockmann, Alireza Nameni, Christian Panse^*, Ralph Schlapbach, Ludwig Lautenbacher, Matthias Mattanovich, Alexey Nesvizhskii, Bart Van Puyvelde, Jonas Scheid, Veit Schwämmle, Maximilian Strauss, Anna Klimovskaia Susmelj, Matthew The, Henry Webel, Mathias Wilhelm, Dirk WinkelhardtWitold E. Wolski, Muyao Xi

^*Corresponding author for this work

Research output: Contribution to journal › Editorial › Research

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Abstract

The 2023 European Bioinformatics Community for Mass Spectrometry (EuBIC-MS) Developers Meeting was held from January 15th to January 20th, 2023, in Congressi Stefano Franscin at Monte Verità in Ticino, Switzerland. The participants were scientists and developers working in computational mass spectrometry (MS), metabolomics, and proteomics. The 5-day program was split between introductory keynote lectures and parallel hackathon sessions focusing on “Artificial Intelligence in proteomics” to stimulate future directions in the MS-driven omics areas. During the latter, the participants developed bioinformatics tools and resources addressing outstanding needs in the community. The hackathons allowed less experienced participants to learn from more advanced computational MS experts and actively contribute to highly relevant research projects. We successfully produced several new tools applicable to the proteomics community by improving data analysis and facilitating future research.

Original language	English
Article number	105246
Journal	Journal of Proteomics
Volume	305
Number of pages	7
ISSN	1874-3919
DOIs	https://doi.org/10.1016/j.jprot.2024.105246
Publication status	Published - 2024

Bibliographical note

Publisher Copyright:
© 2024 The Authors

Keywords

Artificial intelligence
Benchmark development
Bioinformatics
Computational mass spectrometry
Deep learning
Mass spectrometry
Metabolomics
Metaproteomics
Predicted spectra
Proteomics
Spectrum clustering
Visualization

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10.1016/j.jprot.2024.105246Licence: CC BY

1-s2.0-S1874391924001787-mainFinal published version, 1.27 MBLicence: CC BY

Cite this

Beltrao, P., Van Den Bossche, T., Gabriels, R., Holstein, T., Kockmann, T., Nameni, A., Panse, C., Schlapbach, R., Lautenbacher, L., Mattanovich, M., Nesvizhskii, A., Van Puyvelde, B., Scheid, J., Schwämmle, V., Strauss, M., Susmelj, A. K., The, M., Webel, H., Wilhelm, M., ... Xi, M. (2024). Proceedings of the EuBIC-MS developers meeting 2023. Journal of Proteomics, 305, Article 105246. https://doi.org/10.1016/j.jprot.2024.105246

Beltrao, P, Van Den Bossche, T, Gabriels, R, Holstein, T, Kockmann, T, Nameni, A, Panse, C, Schlapbach, R, Lautenbacher, L, Mattanovich, M, Nesvizhskii, A, Van Puyvelde, B, Scheid, J, Schwämmle, V, Strauss, M, Susmelj, AK, The, M, Webel, H, Wilhelm, M, Winkelhardt, D, Wolski, WE & Xi, M 2024, 'Proceedings of the EuBIC-MS developers meeting 2023', Journal of Proteomics, vol. 305, 105246. https://doi.org/10.1016/j.jprot.2024.105246

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abstract = "The 2023 European Bioinformatics Community for Mass Spectrometry (EuBIC-MS) Developers Meeting was held from January 15th to January 20th, 2023, in Congressi Stefano Franscin at Monte Verit{\`a} in Ticino, Switzerland. The participants were scientists and developers working in computational mass spectrometry (MS), metabolomics, and proteomics. The 5-day program was split between introductory keynote lectures and parallel hackathon sessions focusing on “Artificial Intelligence in proteomics” to stimulate future directions in the MS-driven omics areas. During the latter, the participants developed bioinformatics tools and resources addressing outstanding needs in the community. The hackathons allowed less experienced participants to learn from more advanced computational MS experts and actively contribute to highly relevant research projects. We successfully produced several new tools applicable to the proteomics community by improving data analysis and facilitating future research.",

keywords = "Artificial intelligence, Benchmark development, Bioinformatics, Computational mass spectrometry, Deep learning, Mass spectrometry, Metabolomics, Metaproteomics, Predicted spectra, Proteomics, Spectrum clustering, Visualization",

author = "Pedro Beltrao and {Van Den Bossche}, Tim and Ralf Gabriels and Tanja Holstein and Tobias Kockmann and Alireza Nameni and Christian Panse and Ralph Schlapbach and Ludwig Lautenbacher and Matthias Mattanovich and Alexey Nesvizhskii and {Van Puyvelde}, Bart and Jonas Scheid and Veit Schw{\"a}mmle and Maximilian Strauss and Susmelj, {Anna Klimovskaia} and Matthew The and Henry Webel and Mathias Wilhelm and Dirk Winkelhardt and Wolski, {Witold E.} and Muyao Xi",

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year = "2024",

doi = "10.1016/j.jprot.2024.105246",

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journal = "Journal of Proteomics",

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AU - Kockmann, Tobias

AU - Nameni, Alireza

AU - Panse, Christian

AU - Schlapbach, Ralph

AU - Lautenbacher, Ludwig

AU - Mattanovich, Matthias

AU - Nesvizhskii, Alexey

AU - Van Puyvelde, Bart

AU - Scheid, Jonas

AU - Schwämmle, Veit

AU - Strauss, Maximilian

AU - Susmelj, Anna Klimovskaia

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AU - Webel, Henry

AU - Wilhelm, Mathias

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AU - Wolski, Witold E.

AU - Xi, Muyao

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KW - Metabolomics

KW - Metaproteomics

KW - Predicted spectra

KW - Proteomics

KW - Spectrum clustering

KW - Visualization

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