Wout Bittremieux, PhD
Assistant research professor

Wout Bittremieux

University of Antwerp
Campus Middelheim
Middelheimlaan 1
2020 Antwerpen
Belgium


Prof. Dr. Wout Bittremieux is an assistant research professor in the Adrem Data Lab at the University of Antwerp. His research employs advanced computational techniques to solve fundamental biological questions, by developing algorithmic solutions and machine learning methods for the analysis of mass spectrometry-based proteomics and metabolomics data. He has developed several innovative tools to harness novel biological insights from hundreds of millions of mass spectra. His work is ideally positioned at the intersection of bioinformatics, machine learning, and mass spectrometry.

In 2020, Dr. Bittremieux received the prestigious Postdoctoral Career Development Award from the American Society for Mass Spectrometry, in 2021 he was named a "Rising Star in Proteomics and Metabolomics" by the Journal of Proteome Research for demonstrating 'incredible originality and promise for the future of proteomics and metabolomics,' in 2022 he won the Early Career Researcher Manuscript Competition by the Human Proteome Organization, in 2023 he received the Bioinformatics for Mass Spectrometry Award from the European Proteomics Association and the Metabolites Young Investigator Award, and in 2025 he received the Junior Research Parasite Award.

Dr. Bittremieux is an avid contributor to the computational mass spectrometry community. He has published widely in internationally recognized scientific journals, is an active member of the European Bioinformatics Community for Mass Spectrometry (EuBIC-MS), and leads the CompMS interest group of the International Society for Computational Biology (ISCB). Furthermore, he has contributed to the development of mass spectrometry data standards defined by the Proteomics Standards Initiative (PSI) and is an active developer of the Global Natural Products Social Molecular Networking (GNPS) platform, through which his tools reach tens of thousands of monthly users worldwide.

 Curriculum vitae.

Publications

See also Google Scholar.

2024

  • Proceeding MassSpecGym: A benchmark for the discovery and identification of molecules.   

    Roman Bushuiev, Anton Bushuiev, Niek F. de Jonge, Adamo Young, Fleming Kretschmer, Raman Samusevich, Janne Heirman, Fei Wang, Luke Zhang, Kai Dührkop, Marcus Ludwig, Nils A. Haupt, Apurva Kalia, Corinna Brungs, Robin Schmid, Russell Greiner, Bo Wang, David Wishart, Liping Liu, Juho Rousu, Wout Bittremieux, Hannes Röst, Tytus D. Mak, Soha Hassoun, Florian Huber, Justin J.J. van der Hooft, Michael A. Stravs, Sebastian Böcker, Josef Sivic, Tomas Pluskal

    Proceedings of the 38th Conference on Neural Information Processing Systems (NeurIPS 2024) Datasets and Benchmarks Track (2024)

  • Journal A universal language for finding mass spectrometry data patterns.   

    Alan K. Jarmusch, Allegra T. Aron, Daniel Petras, Vanessa V. Phelan, Wout Bittremieux, Deepa D. Acharya, Mohammed M. A. Ahmed, Anelize Bauermeister, Matthew J. Bertin, Paul D. Boudreau, Ricardo M. Borges, Benjamin P. Bowen, Christopher J. Brown, Fernanda O. Chagas, Kenneth D. Clevenger, Mario S. P. Correia, William J. Crandall, Max Crüsemann, Tito Damiani, Oliver Fiehn, Neha Garg, William H Gerwick, Jeffrey R. Gilbert, Daniel Globisch, Paulo Wender P. Gomes, Steffen Heuckeroth, C. Andrew James, Scott A. Jarmusch, Sarvar A. Kakhkhorov, Kyo Bin Kang, Roland D Kersten, Hyunwoo Kim, Riley D. Kirk, Oliver Kohlbacher, Eftychia E. Kontou, Ken Liu, Itzel Lizama-Chamu, Gordon T. Luu, Tal Luzzatto Knaan, Michael T. Marty, Andrew C. McAvoy, Laura-Isobel McCall, Osama G. Mohamed, Omri Nahor, Timo H.J. Niedermeyer, Trent R. Northen, Kirsten E. Overdahl, Tomáš Pluskal, Johannes Rainer, Raphael Reher, Elys Rodriguez, Timo T. Sachsenberg, Laura M. Sanchez, Robin Schmid, Cole Stevens, Zhenyu Tian, Ashootosh Tripathi, Hiroshi Tsugawa, Kozo Nishida, Yuki Matsuzawa, Justin J.J. van der Hooft, Andrea Vicini, Axel Walter, Tilmann Weber, Quanbo Xiong, Tao Xu, Haoqi Nina Zhao, Pieter C. Dorrestein, Mingxun Wang

    Nature Methods, in press (2024)

  • Journal Deep learning methods for de novo peptide sequencing.   

    Wout Bittremieux, Varun Ananth, William E. Fondrie, Carlo Melendez, Marina Pominova, Justin Sanders, Bo Wen, Melih Yilmaz, William Stafford Noble

    Mass Spectrometry Reviews, in press (2024)

  • Journal 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, Jim Shofstahl, Helge Hecht, Pierre-Alain Binz, Shin Kawano, Tim Van Den Bossche, Jeremy Carver, Benjamin A. Neely, Luis Mendoza, Tomi Suomi, Tine Claeys, Thomas Payne, Douwe Schulte, Zhi Sun, Nils Hoffmann, Yunping Zhu, Steffen Neumann, Andrew R. Jones, Nuno Bandeira, Juan Antonio Vizcaíno, Eric W. Deutsch

    Analytical Chemistry, in press (2024)

  • Preprint Empirically establishing drug exposure records directly from untargeted metabolomics data.   

    Haoqi Nina Zhao, Kine Eide Kvitne, Corinna Brungs, Siddharth Mohan, Vincent Charron-Lamoureux, Wout Bittremieux, Runbang Tang, Robin Schmid, Santosh Lamichhane, Yasin El Abiead, Mohammadsobhan S. Andalibi, Helena Mannochio-Russo, Madison Ambre, Nicole E. Avalon, MacKenzie Bryant, Andrés Mauricio Caraballo-Rodríguez, Martin Casas Maya, Loryn Chin, Ronald J. Ellis, Donald Franklin, Sagan Girod, Paulo Wender P. Gomes, Lauren Hansen, Robert Heaton, Jennifer E. Iudicello, Alan K. Jarmusch, Lora Khatib, Scott Letendre, Sarolt Magyari, Daniel McDonald, Ipsita Mohanty, Andrés Cumsille, David J. Moore, Prajit Rajkumar, Dylan H. Ross, Harshada Sapre, Mohammad Reza Zare Shahneh, Sydney P. Thomas, Caitlin Tribelhorn, Helena M. Tubb, Corinn Walker, Crystal X. Wang, Shipei Xing, Jasmine Zemlin, Simone Zuffa, David S. Wishart, Rima Kaddurah-Daouk, Mingxun Wang, Manuela Raffatellu, Karsten Zengler, Tomáš Pluskal, Libin Xu, Rob Knight, Shirley M. Tsunoda, Pieter C. Dorrestein

    bioRxiv (2024)

  • Proceeding RapidOMS: FPGA-Based open modification spectral library searching with HD computing.   

    Sumukh Pinge, Weihong Xu, Wout Bittremieux, Niema Moshiri, Sang-Woo Jun, Tajana Rosing

    Proceedings of the 2024 IEEE Biomedical Circuits and Systems Conference - BioCAS 2024 (2024)

  • Journal Accounting for digestion enzyme bias in Casanovo.   

    Carlo Melendez, Justin Sanders, Melih Yilmaz, Wout Bittremieux, William E. Fondrie, Sewoong Oh, William Stafford Noble

    Journal of Proteome Research 23, 4761–4769 (2024)

  • Preprint pyOpenMS-viz: Streamlining mass spectrometry data visualization with pandas.   

    Justin Sing, Joshua Charkow, Axel Walter, Mingxuan Gao, Tom David Muller, Wout Bittremieux, Timo Sachsenberg, Hannes Röst

    Research Square (2024)

  • Journal Reusability report: Annotating metabolite mass spectra with domain-inspired chemical formula transformers.   

    Janne Heirman, Wout Bittremieux

    Nature Machine Intelligence (2024)

  • Journal Machine learning strategies to tackle data challenges in mass spectrometry-based proteomics.   

    Ceder Dens, Charlotte Adams, Kris Laukens, Wout Bittremieux

    Journal of the American Society for Mass Spectrometry 35, 2143–2155 (2024)

  • Journal DRAM-based acceleration of open modification search for mass spectrometry-based proteomics.   

    Jaeyoung Kang, Weihong Xu, Wout Bittremieux, Niema Moshiri, Tajana Rosing

    IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems 43, 2592–2605 (2024)

  • Journal Semisupervised learning to boost hERG, Nav1.5, and Cav1.2 cardiac ion channel toxicity prediction by mining a large unlabeled small molecule data set.   

    Issar Arab, Kris Laukens, Wout Bittremieux

    Journal of Chemical Information and Modeling 64, 6410–6420 (2024)

  • Journal Communicating mass spectrometry quality information in mzQC with Python, R, and Java.   

    Chris Bielow, Nils Hoffmann, David Jimenez-Morales, Tim Van Den Bossche, Juan Antonio Vizcaíno, David L. Tabb, Wout Bittremieux, Mathias Walzer

    Journal of the American Society for Mass Spectrometry 35, 1875–1882 (2024)

  • Journal Sequence-to-sequence translation from mass spectra to peptides with a transformer model.   

    Melih Yilmaz*, William E. Fondrie*, Wout Bittremieux*, Carlo F. Melendez, Rowan Nelson, Varun Ananth, Sewoong Oh, William Stafford Noble

    Nature Communications 15, 6427 (2024)

  • Journal Fragment ion intensity prediction improves the identification rate of non-tryptic peptides in timsTOF.   

    Charlotte Adams, Wassim Gabriel, Kris Laukens, Mario Picciani, Mathias Wilhelm, Wout Bittremieux*, Kurt Boonen*

    Nature Communications 15, 3956 (2024)

  • Journal Machine learning-based peptide-spectrum match rescoring opens up the immunopeptidome.   

    Charlotte Adams, Kris Laukens, Wout Bittremieux, Kurt Boonen

    PROTEOMICS 24, 2300336 (2024)

  • Journal From data to discovery: The essential role of computational tools in proteomics.   

    Wout Bittremieux

    PROTEOMICS 24, 2300081 (2024)

  • Journal Benchmarking of small molecule feature representations for hERG, Nav1.5, and Cav1.2 cardiotoxicity prediction.   

    Issar Arab, Kristof Egghe, Kris Laukens, Ke Chen, Khaled Barakat, Wout Bittremieux

    Journal of Chemical Information and Modeling 64, 2515–2527 (2024)

  • Journal The underappreciated diversity of bile acid modifications.   

    Ipsita Mohanty, Helena Mannochio-Russo, Yasin El Abiead, Joshua V. Schweer, Wout Bittremieux, Shipei Xing, Robin Schmid, Simone Zuffa, Felipe Vasquez, Valentina B. Muti, Jasmine Zemlin, Omar E. Tovar-Herrera, Sarah Moraïs, Dhimant Desai, Shantu Amin, Imhoi Koo, Christoph W. Turck, Itzhak Mizrahi, Tao Huan, Andrew D. Patterson, Dionicio Siegel, Lee R. Hagey, Mingxun Wang, Allegra T. Aron, Pieter Dorrestein

    Cell 187, 1801–1818 (2024)

  • Proceeding SpecHD: Hyperdimensional computing framework for FPGA-based mass spectrometry clustering.   

    Sumukh Pinge, Weihong Xu, Jaeyoung Kang, Tianqi Zhang, Niema Moshiri, Wout Bittremieux, Tajana Rosing

    Proceedings of the 2024 Design, Automation & Test in Europe Conference - DATE 2024 (2024)

  • Preprint Molecular structure discovery for untargeted metabolomics using biotransformation rules and global molecular networking.   

    Margaret R. Martin, Wout Bittremieux, Soha Hassoun

    bioRxiv (2024)

    • 2023

  • Journal Open access repository-scale propagated nearest neighbor suspect spectral library for untargeted metabolomics.   

    Wout Bittremieux, Nicole E. Avalon, Sydney P. Thomas, Sarvar A. Kakhkhorov, Alexander A. Aksenov, Paulo Wender Portal Gomes, Christine M. Aceves, Andres Mauricio Caraballo Rodriguez, Julia M. Gauglitz, William H. Gerwick, Tao Huan, Alan K. Jarmusch, Rima F. Kaddurah-Daouk, Kyo Bin Kang, Hyun Woo Kim, Todor Kondic, Helena Mannochio-Russo, Michael J. Meehan, Alexey Melnik, Louis-Felix Nothias, Claire O'Donovan, Morgan Panitchpakdi, Daniel Petras, Robin Schmid, Emma L. Schymanski, Justin J. J. van der Hooft, Kelly C. Weldon, Shipei Xing, Heejung Yang, Jasmine Zemlin, Mingxun Wang, Pieter C. Dorrestein

    Nature Communications 14, 8488 (2023)

    "Top 25 Health Sciences Articles of 2023" by Nature Communications

    2025 Junior Research Parasite Award

  • Preprint A cross-attention transformer encoder for paired sequence data.   

    Ceder Dens, Kris Laukens, Pieter Meysman, Wout Bittremieux

    bioRxiv (2023)

  • Journal The pitfalls of negative data bias for the T-cell epitope specificity challenge.   

    Ceder Dens, Kris Laukens, Wout Bittremieux*, Pieter Meysman*

    Nature Machine Intelligence 5, 1060–1062 (2023)

  • Journal Accelerating open modification spectral library searching on tensor core in high-dimensional space.   

    Jaeyoung Kang, Weihong Xu, Wout Bittremieux, Niema Moshiri, Tajana Rosing

    Bioinformatics 22, btad404 (2023)

  • Journal Interpretable deep learning to uncover the molecular binding patterns determining TCR–epitope interactions.   

    Ceder Dens, Wout Bittremieux, Fabio Affaticati, Kris Laukens, Pieter Meysman

    ImmunoInformatics 11, 100027 (2023)

  • Journal HyperSpec: Ultra-fast mass spectra clustering in hyperdimensional space.   

    Weihong Xu, Jaeyoung Kang, Wout Bittremieux, Niema Moshiri, Tajana Rosing

    Journal of Proteome Research 22, 1639–1648 (2023)

  • Journal Unified and standardized mass spectrometry data processing in Python using spectrum_utils.   

    Wout Bittremieux, Lev Levitsky, Matteo Pilz, Timo Sachsenberg, Florian Huber, Mingxun Wang, Pieter C. Dorrestein

    Journal of Proteome Research 22, 625–631 (2023)

  • Journal Semisupervised machine learning for sensitive open modification spectral library searching.   

    Issar Arab, William E. Fondrie, Kris Laukens, Wout Bittremieux

    Journal of Proteome Research 22, 585–593 (2023)

  • Journal The 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, Sylvie Ricard-Blum, Henning Hermjakob, Steffen Neumann, Tytus D. Mak, Shin Kawano, Luis Mendoza, Tim Van Den Bossche, Ralf Gabriels, Nuno Bandeira, Jeremy Carver, Benjamin Pullman, Zhi Sun, Nils Hoffmann, Jim Shofstahl, Yunping Zhu, Luana Licata, Federica Quaglia, Silvio C.E. Tosatto, and Sandra E. Orchard

    Journal of Proteome Research 22, 287–301 (2023)

2022

  • Journal Open modification searching of SARS-CoV-2-human protein interaction data reveals novel viral modification sites.   

    Charlotte Adams, Kurt Boonen, Kris Laukens, Wout Bittremieux

    Molecular & Cellular Proteomics 21, 100425 (2022)

  • Journal Standardized multi-omics of Earth's microbiomes reveals microbial and metabolite diversity.   

    Justin P. Shaffer, Louis-Félix Nothias, Luke R. Thompson, Jon G. Sanders, Rodolfo A. Salido, Sneha P. Couvillion, Asker D. Brejnrod, Shi Huang, Franck Lejzerowicz, Holly L. Lutz, Qiyun Zhu, Cameron Martino, James T. Morton, Smruthi Karthikeyan, Mélissa Nothias-Esposito, Kai Dührkop, Sebastian Böcker, Hyunwoo Kim, Alexander A. Aksenov, Wout Bittremieux, Jeremiah J. Minich, Clarisse Marotz, MacKenzie M. Bryant, Karenina Sanders, Tara Schwartz, Greg Humphrey, Yoshiki Vásquez-Baeza, Anupriya Tripathi, Laxmi Parida, Anna Paola Carrieri, Niina Haiminen, Kristen L. Beck, Promi Das, Antonio González, Daniel McDonald, Søren M. Karst, Mads Albertsen, Gail Ackermann, Jeff DeReus, Torsten Thomas, Daniel Petras, Ashley Shade, James Stegen, Se Jin Song, Thomas O. Metz, Austin D. Swafford, Pieter C. Dorrestein, Janet K. Jansson, Jack A. Gilbert, Rob Knight, the Earth Microbiome Project 500 (EMP500) Consortium

    Nature Microbiology 7, 2128-2150 (2022)

  • Journal The critical role that spectral libraries play in capturing the metabolomics community knowledge. 

    Wout Bittremieux, Mingxun Wang, Pieter C. Dorrestein

    Metabolomics 18, 94 (2022)

  • Journal Four layer multi-omics reveals molecular responses to aneuploidy in Leishmania.   

    Bart Cuypers, Pieter Meysman, Ionas Erb, Wout Bittremieux, Dirk Valkenborg, Geert Baggerman, Inge Mertens, Shyam Sundar, Basudha Khanal, Cedric Notredame, Jean-Claude Dujardin, Malgorzata Domagalska, Kris Laukens

    PLOS Pathogens 18, e1010848 (2022)

  • Proceeding Massively parallel open modification spectral library searching with hyperdimensional computing.   

    Jaeyoung Kang, Weihong Xu, Wout Bittremieux, Tajana Rosing

    Proceedings of the 31st International Conference on Parallel Architectures and Compilation Techniques - PACT 2022 (2022)

  • Journal Comparison of cosine, modified cosine, and neutral loss based spectral alignment for discovery of structurally related molecules.   

    Wout Bittremieux*, Robin Schmid*, Florian Huber, Justin J.J. van der Hooft, Mingxun Wang, Pieter C. Dorrestein

    Journal of the American Society for Mass Spectrometry 33, 1733–1744 (2022)

  • Journal Native metabolomics identifies the rivulariapeptolide family of protease inhibitors.   

    Raphael Reher, Allegra T. Aron, Pavla Fajtova, Chenxi Liu, Ido Y. Ben Shalom, Wout Bittremieux, Mingxun Wang, Marie L. Matos-Hernandez, Kelsey L. Alexander, Eduardo J. Caro-Diaz, C. Benjamin Naman, Pieter C. Dorrestein, Anthony J. O'Donoghue, William H. Gerwick, Daniel Petras

    Nature Communications 13, 4619 (2022)

  • Proceeding De novo mass spectrometry peptide sequencing with a transformer model.   

    Melih Yilmaz, William E. Fondrie, Wout Bittremieux, Sewoong Oh, William Stafford Noble

    Proceedings of the 39th International Conference on Machine Learning - ICML 2022 (2022)

  • Journal Enhancing untargeted metabolomics using metadata-based source annotation.   

    Julia M. Gauglitz*, Kiana A. West*, Wout Bittremieux*, Candace L. Williams, Kelly C. Weldon, Morgan Panitchpakdi, Francesca Di Ottavio, Christine M. Aceves, Elizabeth Brown, Nicole C. Sikora, Alan K. Jarmusch, Cameron Martino, Anupriya Tripathi, Michael J. Meehan, Kathleen Dorrestein, Justin P. Shaffer, Roxana Coras, Fernando Vargas, Lindsay DeRight Goldasich, Tara Schwartz, MacKenzie Bryant, Gregory Humphrey, Abigail J. Johnson, Katharina Spengler, Pedro Belda-Ferre, Edgar Diaz, Daniel McDonald, Qiyun Zhu, Emmanuel O. Elijah, Mingxun Wang, Clarisse Marotz, Kate E. Sprecher, Daniela Vargas-Robles, Dana Withrow, Gail Ackermann, Lourdes Herrera, Barry J. Bradford, Lucas Maciel Mauriz Marques, Juliano Geraldo Amaral, Rodrigo Moreira Silva, Flavio Protasio Veras, Thiago Mattar Cunha, Rene Donizeti Ribeiro Oliveira, Paulo Louzada-Junior, Robert H. Mills, Paulina K. Piotrowski, Stephanie L. Servetas, Sandra M. Da Silva, Christina M. Jones, Nancy J. Lin, Katrice A. Lippa, Scott A. Jackson, Rima Kaddurah Daouk, Douglas Galasko, Parambir S. Dulai, Tatyana I. Kalashnikova, Curt Wittenberg, Robert Terkeltaub, Megan M. Doty, Jae H. Kim, Kyung E. Rhee, Julia Beauchamp-Walters, Kenneth P. Wright Jr, Maria Gloria Dominguez-Bello, Mark Manary, Michelli F. Oliveira, Brigid S. Boland, Norberto Peporine Lopes, Monica Guma, Austin D. Swafford, Rachel J. Dutton, Rob Knight, Pieter C. Dorrestein

    Nature Biotechnology 40, 1774–1779 (2022)

  • Journal A learned embedding for efficient joint analysis of millions of mass spectra.   

    Wout Bittremieux, Damon H. May, Jeffrey Bilmes, William Stafford Noble

    Nature Methods 19, 675–678 (2022)

    "Early Career Researcher Manuscript Competition" winner by the Human Proteome Organization

  • Journal A neural network for large-scale clustering of peptide mass spectra. 

    Nature Methods 19, 658–659 (2022)

  • Journal A comprehensive evaluation of consensus spectrum generation methods in proteomics.   

    Xiyang Luo*, Wout Bittremieux*, Johannes Griss, Eric W. Deutsch, Timo Sachsenberg, Lev I. Levitsky, Mark V. Ivanov, Julia A. Bubis, Ralf Gabriels, Henry Webel, Aniel Sanchez, Mingze Bai, Lukas Käll, Yasset Perez-Riverol

    Journal of Proteome Research 21, 1566–1574 (2022)

  • Journal Proteomics Standards Initiatives ProForma 2.0: Unifying the encoding of Proteoforms and Peptidoforms.   

    Richard D. LeDuc, Eric W. Deutsch, Pierre-Alain Binz, Ryan T. Fellers, Anthony J. Cesnik, Joshua A. Klein, Tim Van Den Bossche, Ralf Gabriels, Arshika Yalavarthi, Yasset Perez-Riverol, Jeremy Carver, Wout Bittremieux, Shin Kawano, Benjamin Pullman, Nuno Bandeira, Neil L. Kelleher, Paul M. Thomas, Juan Antonio Vizcaíno

    Journal of Proteome Research 21, 1189–1195 (2022)

  • Journal Physicochemical properties determining drug detection in skin.   

    Wout Bittremieux*, Rohit S. Advani*, Alan K. Jarmusch, Shaden Aguirre, Aileen Lu, Pieter C. Dorrestein, Shirley M. Tsunoda

    Clinical and Translational Science 15, 761–770 (2022)

2021

  • Journal ppx: Programmatic access to proteomics data repositories.   

    William E. Fondrie, Wout Bittremieux, William Stafford Noble

    Journal of Proteome Research 20, 4621–4624 (2021)

  • Journal Current challenges for unseen-epitope TCR interaction prediction and a new perspective derived from image classification.   

    Pieter Moris, Joey De Pauw, Anna Postovskaya, Sofie Gielis, Nicolas De Neuter, Wout Bittremieux, Benson Ogunjimi, Kris Laukens, Pieter Meysman

    Briefings in Bioinformatics 22, bbaa318 (2021)

  • Journal Universal Spectrum Identifier for mass spectra.   

    Eric W. Deutsch, Yasset Perez-Riverol, Jeremy Carver, Shin Kawano, Luis Mendoza, Tim Van Den Bossche, Ralf Gabriels, Pierre-Alain Binz, Benjamin Pullman, Zhi Sun, Jim Shofstahl, Wout Bittremieux, Tytus Mak, Joshua Klein, Yunping Zhu, Henry Lam, Juan Antonio Vizcaino, Nuno Bandeira

    Nature Methods 18, 768–770 (2021)

  • Journal Large-scale tandem mass spectrum clustering using fast nearest neighbor searching.   

    Wout Bittremieux, Kris Laukens, William Stafford Noble, Pieter C. Dorrestein

    Rapid Communications in Mass Spectrometry, e9153 (2021)

  • Journal Current and future deep learning algorithms for MS/MS-based small molecule structure elucidation. 

    Youzhong Liu, Wouter Heyndrickx, Wout Bittremieux, Kris Laukens, Thomas De Vijlder

    Rapid Communications in Mass Spectrometry, e9120 (2021)

  • Journal The European Bioinformatics Community for Mass Spectrometry (EuBIC-MS): An open community for bioinformatics training and research. 

    Wout Bittremieux, David Bouyssié, Viktoria Dorfer, Marie Locard-Paulet, Yasset Perez-Riverol, Veit Schwämmle, Julian Uszkoreit, Tim Van Den Bossche

    Rapid Communications in Mass Spectrometry, e9087 (2021)

  • Journal Sharing biological data: Why, when, and how. 

    Samantha L. Wilson, Gregory P. Way, Wout Bittremieux, Jean-Paul Armache, Melissa A. Haendel, Michael M. Hoffman

    FEBS Letters 595, 847–863 (2021)

  • Journal Open science resources for the mass spectrometry-based analysis of SARS-CoV-2.   

    Wout Bittremieux, Charlotte Adams, Kris Laukens, Pieter C. Dorrestein, Nuno Bandeira

    Journal of Proteome Research 20, 1464–1475 (2021)

  • Journal Auto-deconvolution and molecular networking of gas chromatography–mass spectrometry data. 

    Alexander Aksenov, Ivan Laponogov, Zheng Zhang, Sophie Doran, Ilaria Belluomo, Dennis Veselkov, Wout Bittremieux, Louis Felix Nothias, Mélissa Nothias-Esposito, Katherine N. Maloney, Biswapriya Biswavas Misra, Alexey V. Melnik, Kenneth L. Jones II, Kathleen Dorrestein, Morgan Panitchpakdi, Madeleine Ernst, Justin J.J. van der Hooft, Mabel Gonzalez, Chiara Carazzone, Adolfo Amézquita, Chris Callewaert, Jamie Morton, Robert Andrew Quinn, Amina Bouslimani, Andrea Albarracin Orio, Daniel Petras, Andrea Maria Smania, Sneha P. Couvillion, Meagan C. Burnet, Carrie D. Nicora, Erika Zink, Thomas O. Metz, Viatcheslav Artaev, Elizabeth Humston-Fulmer, Rachel Gregor, Michael M. Meijler, Itzhak Mizrahi, Stav Eyal, Brooke Anderson, Rachel J. Dutton, Raphael Lugan, Pauline Le Boulch, Yann Guitton, Stephanie Prevost, Audrey Poirier, Gaud Dervilly, Bruno Le Bizec, Aharon Fait, Noga Sikron, Chao Song, Kelem Gashu, Roxana Coras, Monica Guma, Julia Manasson, Jose U. Scher, Dinesh K. Barupal, Saleh Alseekh, Alisdair Fernie, Alisdair R. Fernie, Reza Mirnezami, Vasilis Vasiliou, Robin Schmid, Roman S. Borisov, Larisa N. Kulikova, Rob Knight, Mingxun Wang, George Hanna, Pieter C. Dorrestein, Kirill Veselkov

    Nature Biotechnology 39, 169–173 (2021)

2020

  • Journal Proceedings of the EuBIC-MS 2020 Developers' Meeting. 

    Christopher Ashwood, Wout Bittremieux, Eric W. Deutsch, Nadezhda T. Doncheva, Viktoria Dorfer, Ralf Gabriels, Vladimir Gorshkov, Surya Gupta, Andrew R. Jones, Lukas Käll, Dominik Kopczynski, Lydie Lane, Ludwig Lautenbacher, Marc Legeay, Marie Locard-Paulet, Bart Mesuere, Yasset Perez-Riverol, Eugen Netz, Julianus Pfeuffer, Timo Sachsenberg, Renee Salz, Patroklos Samaras , Henning Schiebenhoefer, Tobias Schmidt, Veit Schwämmle, Alessio Soggiu, Julian Uszkoreit, Tim Van Den Bossche, Bart Van Puyvelde, Joeri Van Strien, Pieter Verschaffelt, Henry Webel, Sander Willems

    EuPA Open Proteomics 24, 1–6 (2020)

  • Preprint Universal MS/MS visualization and retrieval with the Metabolomics Spectrum Resolver web service.   

    Wout Bittremieux, Christopher Chen, Pieter C. Dorrestein, Emma L. Schymanski, Tobias Schulze, Steffen Neumann, Rene Meier, Simon Rogers, Mingxun Wang

    bioRxiv (2020)

  • Book Identification of epitope-specific T cells in T-cell receptor repertoires. 

    Sofie Gielis, Pieter Moris, Wout Bittremieux, Nicolas De Neuter, Benson Ogunjimi, Kris Laukens, Pieter Meysman

    Bioinformatics for Cancer Immunotherapy 2120, 183–195 (2020)

  • Journal MESSAR: Automated recommendation of metabolite substructures from tandem mass spectra.   

    Youzhong Liu, Aida Mrzic, Pieter Meysman, Thomas De Vijlder, Edwin P. Romijn, Dirk Valkenborg, Wout Bittremieux, Kris Laukens

    PLOS ONE 15, e0226770 (2020)

  • Journal spectrum_utils: A Python package for mass spectrometry data processing and visualization.   

    Wout Bittremieux

    Analytical Chemistry 92, 659–661 (2020)

2019

  • Journal Detection of enriched T cell epitope specificity in full T cell receptor sequence repertoires.   

    Sofie Gielis, Pieter Moris*, Wout Bittremieux*, Nicolas De Neuter, Benson Ogunjimi, Kris Laukens, Pieter Meysman

    Frontiers in Immunology 10, 2820 (2019)

  • Journal Mining the enriched subgraphs for specific vertices in a biological graph. 

    Pieter Meysman, Yvan Saeys, Ehsan Sabaghian, Wout Bittremieux, Yves van de Peer, Bart Goethals, Kris Laukens

    IEEE/ACM Transactions on Computational Biology and Bioinformatics 16, 1496–1507 (2019)

  • Journal 2018 YPIC Challenge: A case study in characterizing an unknown protein sample.   

    Lindsay Pino, Andy Lin, Wout Bittremieux

    Journal of Proteome Research 18, 3936–3943 (2019)

  • Journal Extremely fast and accurate open modification spectral library searching of high-resolution mass spectra using feature hashing and graphics processing units.   

    Wout Bittremieux, Kris Laukens, William Stafford Noble

    Journal of Proteome Research 18, 3792–3799 (2019)

  • Journal Proceedings of the EuBIC Winter School 2019.   

    Dominik Kopczynski, Wout Bittremieux, David Bouyssié, Viktoria Dorfer, Marie Locard-Paulet, Bart Van Puyvelde, Veit Schwämmle, Alessio Soggiu, Sander Willems, Julian Uszkoreit

    EuPA Open Proteomics 22–23, 4–7 (2019)

  • Journal Using expert driven machine learning to enhance dynamic metabolomics data analysis.   

    Charlie Beirnaert, Laura Peeters, Pieter Meysman, Wout Bittremieux, Kenn Foubert, Deborah Custers, Anastasia Van der Auwera, Matthias Cuykx, Luc Pieters, Adrian Covaci, Kris Laukens

    Metabolites 9, 54 (2019)

2018

  • Journal Fast open modification spectral library searching through approximate nearest neighbor indexing.   

    Wout Bittremieux, Pieter Meysman, William Stafford Noble, Kris Laukens

    Journal of Proteome Research 17, 3463–3474 (2018)

    "Rising Star in Proteomics and Metabolomics" awarded by the Journal of Proteome Research

  • Journal Proceedings of the EuBIC Developer's Meeting 2018.   

    Sander Willems, David Bouyssié, Dieter Deforce, Viktoria Dorfer, Vladimir Gorshkov, Dominik Kopczynski, Kris Laukens, Marie Locard-Paulet, Veit Schwämmle, Julian Uszkoreit, Dirk Valkenborg, Marc Vaudel, Wout Bittremieux

    Journal of Proteomics 187, 25–27 (2018)

  • Journal Grasping frequent subgraph mining for bioinformatics applications.   

    Aida Mrzic, Pieter Meysman, Wout Bittremieux, Pieter Moris, Boris Cule, Bart Goethals, Kris Laukens

    BioData Mining 11 (2018)

  • Journal Quality control in mass spectrometry-based proteomics.   

    Wout Bittremieux, David L. Tabb, Francis Impens, An Staes, Evy Timmerman, Lennart Martens, Kris Laukens

    Mass Spectrometry Reviews 37, 697–711 (2018)

  • Journal On the feasibility of mining CD8+ T-cell receptor patterns underlying immunogenic peptide recognition. 

    Nicolas De Neuter, Wout Bittremieux, Charlie Beirnaert, Bart Cuypers, Aida Mrzic, Pieter Moris, Arvid Suls, Viggo Van Tendeloo, Benson Ogunjimi, Kris Laukens, Pieter Meysman

    Immunogenetics 70, 159–168 (2018)

2017

  • Journal Proteomics Standards Initiative: Fifteen years of progress and future work.   

    Eric W. Deutsch, Sandra Orchard, Pierre-Alain Binz, Wout Bittremieux, Martin Eisenacher, Henning Hermjakob, Shin Kawano, Henry Lam, Gerhard Mayer, Gerben Menschaert, Yasset Perez-Riverol, Reza M. Salek, David L. Tabb, Stefan Tenzer, Juan Antonio Vizcaíno, Mathias Walzer, Andrew R. Jones

    Journal of Proteome Research 16, 4288–4298 (2017)

  • Journal A community proposal to integrate proteomics activities in ELIXIR [version 1; referees: 2 approved].   

    Juan Antonio Vizcaíno, Mathias Walzer, Rafael C. Jiménez, Wout Bittremieux, David Bouyssié, Christine Carapito, Fernando Corrales, Myriam Ferro, Albert J.R. Heck, Peter Horvatovich, Martin Hubalek, Lydie Lane, Kris Laukens, Fredrik Levander, Frederique Lisacek, Petr Novak, Magnus Palmblad, Damiano Piovesan, Alfred Pühler, Veit Schwämmle, Dirk Valkenborg, Merlijn van Rijswijk, Jiri Vondrasek, Martin Eisenacher, Lennart Martens, Oliver Kohlbacher

    F1000Research 6, 875 (2017)

  • Journal The Human Proteome Organization–Proteomics Standards Initiative Quality Control working group: Making quality control more accessible for biological mass spectrometry.   

    Wout Bittremieux, Mathias Walzer, Stefan Tenzer, Weimin Zhu, Reza M. Salek, Martin Eisenacher, David L. Tabb

    Analytical Chemistry 89, 4474–4479 (2017)

  • Thesis Computational solutions for quality control of mass spectrometry-based proteomics.   

    Wout Bittremieux

    Universiteit Antwerpen (2017)

  • Journal Computational quality control tools for mass spectrometry proteomics.   

    Wout Bittremieux, Dirk Valkenborg, Lennart Martens, Kris Laukens

    PROTEOMICS 17, 1600159 (2017)

2016

  • Journal Designing biomedical proteomics experiments: State-of-the-art and future perspectives. 

    Evelyne Maes, Pieter Kelchtermans, Wout Bittremieux, Kurt De Grave, Sven de Groeve, Jef Hooyberghs, Inge Mertens, Geert Baggerman, Jan Ramon, Kris Laukens, Lennart Martens, Dirk Valkenborg

    Expert Review of Proteomics 13, 495–511 (2016)

  • Journal Unsupervised quality assessment of mass spectrometry proteomics experiments by multivariate quality control metrics. 

    Wout Bittremieux, Pieter Meysman, Lennart Martens, Dirk Valkenborg, Kris Laukens

    Journal of Proteome Research 15, 1300–1307 (2016)

2015

  • Proceeding Discovery of significantly enriched subgraphs associated with selected vertices in a single graph. 

    Pieter Meysman, Yvan Saeys, Ehsan Sabaghian, Wout Bittremieux, Yves Van de Peer, Bart Goethals, Kris Laukens

    Proceedings of the 14th International Workshop on Data Mining in Bioinformatics - BIOKDD '15 (2015)

  • Journal iMonDB: Mass spectrometry quality control through instrument monitoring. 

    Wout Bittremieux, Hanny Willems, Pieter Kelchtermans, Lennart Martens, Kris Laukens, Dirk Valkenborg

    Journal of Proteome Research 14, 2360–2366 (2015)

  • Journal A primer to frequent itemset mining for bioinformatics.   

    Stefan Naulaerts, Pieter Meysman, Wout Bittremieux, Trung Nghia Vu, Wim Vanden Berghe, Bart Goethals, Kris Laukens

    Briefings in Bioinformatics 16, 216–231 (2015)

2014

  • Journal Efficient reduction of candidate matches in peptide spectrum library searching using the top k most intense peaks. 

    Trung Nghia Vu, Wout Bittremieux, Dirk Valkenborg, Bart Goethals, Filip Lemière, Kris Laukens

    Journal of Proteome Research 13, 4175–4183 (2014)

  • Journal qcML: An exchange format for quality control metrics from mass spectrometry experiments.   

    Mathias Walzer, Lucia Espona Pernas, Sara Nasso, Wout Bittremieux, Sven Nahnsen, Pieter Kelchtermans, Peter Pichler, Henk W. P. van den Toorn, An Staes, Jonathan Vandenbussche, Michael Mazanek, Thomas Taus, Richard A. Scheltema, Christian D. Kelstrup, Laurent Gatto, Bas van Breukelen, Stephan Aiche, Dirk Valkenborg, Kris Laukens, Kathryn S. Lilley, Jesper V. Olsen, Albert J. R. Heck, Karl Mechtler, Ruedi Aebersold, Kris Gevaert, Juan Antonio Vizcaíno, Henning Hermjakob, Oliver Kohlbacher, Lennart Martens

    Molecular & Cellular Proteomics 13, 1905–1913 (2014)

  • Journal jqcML: An open-source Java API for mass spectrometry quality control data in the qcML format. 

    Wout Bittremieux, Pieter Kelchtermans, Dirk Valkenborg, Lennart Martens, Kris Laukens

    Journal of Proteome Research 13, 3484–3487 (2014)

  • Journal Machine learning applications in proteomics research: How the past can boost the future. 

    Pieter Kelchtermans, Wout Bittremieux, Kurt De Grave, Sven Degroeve, Jan Ramon, Kris Laukens, Dirk Valkenborg, Harald Barsnes, Lennart Martens

    PROTEOMICS 14, 353–366 (2014)

Presentations

2024

  • Oral Sequence-to-sequence translation from mass spectra to peptides with a transformer model. 

    EuBIC-MS Seminar on Computational Mass Spectrometry , Barcelona, Spain (September 26, 2024)

  • Invited Learning from repository-scale untargeted metabolomics data. 

    Benelux Metabolomics Days, Ghent, Belgium (September 6, 2024)

  • Invited Learning from repository-scale untargeted metabolomics data. 

    UCR Post-ASMS Symposium, Riverside, CA, USA (June 7, 2024)

  • Workshop Machine learning for proteomics: Challenges, opportunities, and ProteomicsML. 

    ASMS 2024, Anaheim, CA, USA (June 5, 2024)

  • Workshop De novo peptide sequencing: Breakthroughs and challenges. 

    ASMS 2024, Anaheim, CA, USA (June 4, 2024)

  • Poster Enhanced spectrum clustering for molecular networking. 

    ASMS 2024, Anaheim, CA, USA (June 3, 2024)

  • Invited Improved immunopeptidome analysis using timsTOF fragment ion intensity prediction. 

    OMICS Research Day, Antwerp, Belgium (May 15, 2024)

  • Invited Molecules of mystery: A journey of computational mass spectrometry and artificial intelligence. 

    Faculty of Science Research Day, Antwerp, Belgium (February 8, 2024)

2023

  • Invited Bioinformatics to explore the molecular universe. 

    EuPA ECR Day (October 5, 2023)

  • Invited Sequence-to-sequence translation from mass spectra to peptides with a transformer model. 

    Proteomics ONLINE (September 28, 2023)

  • Workshop Machine learning applications for immunopeptidomics analysis. 

    Bioinformatics Hub, HUPO 2023 World Congress, Busan, South Korea (September 18, 2023)

  • Invited Deep learning to uncover the immunopeptidome. 

    BMSS 2023, Manchester, United Kingdom (September 14, 2023)

  • Oral Improved immunopeptidome analysis using timsTOF fragment ion intensity prediction. 

    BSPR/EuPA 2023, Newcastle upon Tyne, United Kingdom (July 19, 2023)

  • Invited Leveraging public mass spectrometry for molecular discovery from millions of mass spectra. 

    Biomina Lunch Talks, Antwerp, Belgium (June 30, 2023)

  • Poster Unified and standardized mass spectrometry data processing in Python using spectrum_utils. 

    ASMS 2023, Houston, TX, USA (June 5, 2023)

2022

  • Oral A learned embedding for efficient joint analysis of millions of mass spectra. 

    HUPO 2022 World Congress, Cancun, Mexico (December 7, 2022)

  • Poster Semi-supervised rescoring for open modification searching reveals protein modifications during SARS-CoV-2 infection. 

    HUPO 2022 World Congress, Cancun, Mexico (December 6, 2022)

  • Poster Comparison of spectrum similarity measures for discovery of structurally related molecules. 

    ASMS 2022, Minneapolis, MN, USA (June 8, 2022)

  • Invited A learned embedding for efficient joint analysis of millions of mass spectra. 

    Best of US HUPO 2022 (May 3, 2022)

  • Invited Leveraging public untargeted metabolomics data to propagate structurally related molecule annotations to millions of MS/MS spectra. 

    VIB Applied Bioinformatics in Life Sciences, Leuven, Belgium (March 11, 2022)

  • Oral A learned embedding for efficient joint analysis of millions of mass spectra. 

    US HUPO 2022, Charleston, SC, USA (March 1, 2022)

  • Poster Leveraging public untargeted metabolomics data to propagate annotations to millions of MS/MS spectra. 

    US HUPO 2022, Charleston, SC, USA (March 1, 2022)

2021

  • Poster Repository scale propagated spectral library of suspects for untargeted metabolomics. 

    ASMS 2021, Philadelphia, PA, USA (November 2, 2021)

2020

  • Oral Repository-scale propagated spectral library of suspects. 

    SoCal Science @Home Lollapalooza (December 1, 2020)

  • Oral Deep neural network embedding for efficient repository-scale analysis of hundreds of millions of mass spectra. 

    ASMS 2020 Reboot (June 8, 2020)

  • Oral Identifying millions of protein modifications using GPU-powered approximate nearest neighbor searching. 

    GPU Technology Conference (March 26, 2020)

2019

  • Poster A learned embedding for efficient joint analysis of millions of mass spectra. 

    Machine Learning in Computational Biology, Vancouver, BC, Canada (December 14, 2019)

  • Poster ANN-SoLo: Extremely fast and accurate open modification spectral library searching. 

    ASMS 2019, Atlanta, GA, USA (June 3, 2019)

2018

  • Poster Fast open modification spectral library searching through approximate nearest neighbor indexing. 

    Department of Genome Sciences retreat, Leavenworth, WA, USA (September 17, 2018)

  • Oral Fast open modification spectral library searching through approximate nearest neighbor indexing. 

    Cascadia Proteomics Symposium, Seattle, WA, USA (July 23, 2018)

2017

  • Poster Mass spectrometry proteomics: Ready for the deep learning (r)evolution? 

    ASMS 2017, Indianapolis, IN, USA (June 8, 2017)

  • Poster Towards the smart lab: A comprehensive approach to mass spectrometry quality control. 

    ASMS 2017, Indianapolis, IN, USA (June 8, 2017)

  • Invited Shedding light on complex mass spectrometry proteomics processes through advanced data mining. 

    Faculty of Science Research Day, Antwerp, Belgium (January 13, 2017)

2016

  • Oral Git: How version control can power your research. 

    Biomina Lunch Talks, Antwerp, Belgium (June 24, 2016)

  • Oral Optimized open modification spectral library searching using approximate nearest neighbor techniques. 

    ASMS 2016, San Antonio, TX, USA (June 9, 2016)

  • Poster Automatic quality assessment of mass spectrometry experiments by multivariate quality control metrics. 

    ASMS 2016, San Antonio, TX, USA (June 9, 2016)

2015

  • Oral Approaches for mass spectrometry quality control. 

    Biomina Research Day, Antwerp, Belgium (December 9, 2015)

  • Oral Analysis of mass spectrometry quality control metrics. 

    Benelux Bioinformatics Conference, Antwerp, Belgium (December 7, 2015)

    Outstanding oral presentation award

  • Oral Precursor-free and fast spectral library search using approximate nearest neighbor techniques. 

    Benelux Bioinformatics Conference Student Council Symposium, Antwerp, Belgium (December 6, 2015)

  • Poster Mass spectrometry quality control: Instrument monitoring and pattern mining insights. 

    ASMS 2015, St. Louis, MO, USA (June 2, 2015)

  • Workshop iMonDB: Mass spectrometry instrument monitoring for quality control.

    Methods and tools for intra- and inter-experiment LC MS performance tracking workshop, ASMS 2015, St. Louis, MO, USA (June 1, 2015)

2014

  • Poster A comprehensive approach to mass spectrometry quality control. 

    Two-day symposium of the Belgian Proteomics Association, Brussels, Belgium (December 18, 2014)

  • Oral Pattern mining of mass spectrometry quality control data. 

    Benelux Bioinformatics Conference, Luxembourg, Luxembourg (December 9, 2014)

  • Poster Pattern mining of mass spectrometry quality control data. 

    European Conference on Computational Biology, Strasbourg, France (September 7, 2014)

  • Poster Mining mass spectrometry quality control data. 

    ASMS 2014, Baltimore, MD, USA (June 16, 2014)

  • Oral Collecting and mining mass spectrometry quality control data. 

    Biomina Research Day, Antwerp, Belgium (February 20, 2014)

2013

  • Poster jqcML: An open-source Java API for mass spectrometry quality control data in the qcML format. 

    Benelux Bioinformatics Conference, Brussels, Belgium (December 9, 2013)

Selected software

See also GitHub.

GLEAMS
GLEAMS
Siamese deep neural network to embed mass spectra into a latent space.
ANN-SoLo
ANN-SoLo
Fast and sensitive GPU-powered open modification spectral library searching.
falcon
falcon
Large-scale tandem mass spectrum clustering using fast nearest neighbor searching.
spectrum_utils
spectrum_utils
Python package for efficient mass spectrum processing and visualization.