Ghent University Academic Bibliography

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Unlocking the next decade of proteomics with standardized, structured metadata

Tim Van Den Bossche (UGent) , Ananth Prakash, Tine Claeys (UGent) , Juan Antonio Vizcaíno and Lennart Martens (UGent)

(2026) JOURNAL OF PROTEOME RESEARCH. 25(2). p.556-561
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Establishing the ELIXIR microbiome community

Robert D. Finn, Bachir Balech, Josephine Burgin, Physilia Chua, Erwan Corre, Cymon J. Cox, Claudio Donati, Vitor Martins dos Santos, Bruno Fosso, John Hancock, et al.

(2025) F1000RESEARCH. 13. p.1-47
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MzPeak : designing a scalable, interoperable, and future-ready mass spectrometry data format

Tim Van Den Bossche (UGent) , Theodore Alexandrov, Aivett Bilbao, Wout Bittremieux, Federico Ivan Brigante, Matthew Chase Chambers, Joshua Charkow, Eric Deutsch, Andrew W. Dowsey, Yasin El Abiead, et al.

(2025) JOURNAL OF PROTEOME RESEARCH. 24(11). p.5329-5335
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- Miscellaneous
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An expanded reference catalog of translated open reading frames for biomedical research

Sonia Chothani, Jorge Ruiz-Orera, Jack A. S. Tierney, Jim Clauwaert, Eric W Deutsch, M. Mar Alba, Julie L. Aspden, Pavel V. Baranov, Ariel Alejandro Bazzini, Elspeth A. Bruford, et al.

(2025) bioRxiv.
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Translon : a single term for translated regions

Michał I. Świrski, Jack A. S. Tierney, M. Mar Albà, Dmitry E. Andreev, Julie L. Aspden, John F. Atkins, Michal Bassani-Sternberg, Marla J. Berry, Stefano Biffo, Kathleen Boris-Lawrie, et al.

(2025) NATURE METHODS. 22(10). p.2002-2006
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The proteomics standards initiative standardized formats for spectral libraries and fragment ion peak annotations : mzSpecLib and mzPAF

Joshua Klein, Henry Lam, Tytus D. Mak, Wout Bittremieux, Yasset Perez-Riverol, Ralf Gabriels (UGent) , Jim Shofstahl, Helge Hecht, Pierre-Alain Binz, Shin Kawano, et al.

(2024) ANALYTICAL CHEMISTRY. 96(46). p.18491-18501
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High-quality peptide evidence for annotating non-canonical open reading frames as human proteins

Eric W Deutsch, Leron W Kok, Jonathan M Mudge, Jorge Ruiz-Orera, Ivo Fierro-Monti, Zhi Sun, Jennifer G Abelin, M Mar Alba, Julie L Aspden, Ariel A Bazzini, et al.

(2024) bioRxiv.
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lesSDRF is more : maximizing the value of proteomics data through streamlined metadata annotation

Tine Claeys (UGent) , Tim Van Den Bossche (UGent) , Yasset Perez-Riverol, Kris Gevaert (UGent) , Juan Antonio Vizcaíno and Lennart Martens (UGent)

(2023) NATURE COMMUNICATIONS. 14(1).
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ProteomicsML : an online platform for community-curated data sets and tutorials for machine learning in proteomics

Tobias G. Rehfeldt, Ralf Gabriels (UGent) , Robbin Bouwmeester (UGent) , Siegfried Gessulat, Benjamin A. Neely, Magnus Palmblad, Yasset Perez-Riverol, Tobias Schmidt, Juan Antonio Vizcaíno and Eric W. Deutsch

(2023) JOURNAL OF PROTEOME RESEARCH. 22(2). p.632-636
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Proteomics standards initiative at twenty years : current activities and future work

Eric W. Deutsch, Juan Antonio Vizcaíno, Andrew R. Jones, Pierre-Alain Binz, Henry Lam, Joshua Klein, Wout Bittremieux, Yasset Perez-Riverol, David L. Tabb, Mathias Walzer, et al.

(2023) JOURNAL OF PROTEOME RESEARCH. 22(2). p.287-301

Academic Bibliography

Unlocking the next decade of proteomics with standardized, structured metadata

Establishing the ELIXIR microbiome community

MzPeak : designing a scalable, interoperable, and future-ready mass spectrometry data format

An expanded reference catalog of translated open reading frames for biomedical research

Translon : a single term for translated regions

The proteomics standards initiative standardized formats for spectral libraries and fragment ion peak annotations : mzSpecLib and mzPAF

High-quality peptide evidence for annotating non-canonical open reading frames as human proteins

lesSDRF is more : maximizing the value of proteomics data through streamlined metadata annotation

ProteomicsML : an online platform for community-curated data sets and tutorials for machine learning in proteomics

Proteomics standards initiative at twenty years : current activities and future work

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