Wout Bittremieux, PhD
Postdoctoral researcher

Dorrestein Laboratory — University of California San Diego
Skaggs School of Pharmacy and Pharmaceutical Sciences
9500 Gilman Drive
La Jolla, CA 92093-0751
- bittremieux
- bittremieux
- 0000-0002-3105-1359
- wbittremieux AT health DOT ucsd DOT edu
Dr. Wout Bittremieux is a postdoctoral researcher at the Dorrestein Laboratory of the University of California San Diego. 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 analyze large mass spectral data volumes, such as the ANN-SoLo tool for extremely fast open modification searching, the falcon tool for efficient spectrum clustering, and the GLEAMS deep neural network to efficiently process 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, and 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.' 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.
Publications
See also Google Scholar.
2022
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Journal A learned embedding for efficient joint analysis of millions of mass spectra.
Nature Methods, in press (2022)
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Journal Proportional diet readout through reference data-set driven metabolomics.
Nature Biotechnology, in press (2022)
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Proceeding De novo mass spectrometry peptide sequencing with a transformer model.
Proceedings of the 39th International Conference on Machine Learning - ICML 2022 (2022)
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Preprint Open access repository-scale propagated nearest neighbor suspect spectral library for untargeted metabolomics.
bioRxiv (2022)
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Journal A comprehensive evaluation of consensus spectrum generation methods in proteomics.
Journal of Proteome Research (2022)
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Preprint Interpretable deep learning to uncover the molecular binding patterns determining TCR–epitope interactions.
bioRxiv (2022)
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Journal Proteomics Standards Initiatives ProForma 2.0: Unifying the encoding of Proteoforms and Peptidoforms.
Journal of Proteome Research 21, 1189–1195 (2022)
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Preprint Open modification searching of SARS-CoV-2-human protein interaction data reveals novel viral modification sites.
bioRxiv (2022)
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Journal Physicochemical properties determining drug detection in skin.
Clinical and Translational Science 15, 761–770 (2022)
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Preprint Multi-omics profiling of Earth's biomes reveals that microbial and metabolite composition are shaped by the environment.
bioRxiv (2022)
2021
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Preprint Four layer multi-omics reveals molecular responses to aneuploidy in Leishmania.
bioRxiv (2021)
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Preprint Native metabolomics identifies the rivulariapeptolide family of protease inhibitors.
bioRxiv (2021)
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Journal ppx: Programmatic access to proteomics data repositories.
Journal of Proteome Research 20, 4621–4624 (2021)
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Journal Current challenges for unseen-epitope TCR interaction prediction and a new perspective derived from image classification.
Briefings in Bioinformatics 22, bbaa318 (2021)
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Journal Universal Spectrum Identifier for mass spectra.
Nature Methods 18, 768–770 (2021)
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Journal Large-scale tandem mass spectrum clustering using fast nearest neighbor searching.
Rapid Communications in Mass Spectrometry, e9153 (2021)
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Journal Current and future deep learning algorithms for MS/MS-based small molecule structure elucidation.
Rapid Communications in Mass Spectrometry, e9120 (2021)
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Journal The European Bioinformatics Community for Mass Spectrometry (EuBIC-MS): An open community for bioinformatics training and research.
Rapid Communications in Mass Spectrometry, e9087 (2021)
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Journal Sharing biological data: Why, when, and how.
FEBS Letters 595, 847–863 (2021)
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Journal Open science resources for the mass spectrometry-based analysis of SARS-CoV-2.
Journal of Proteome Research 20, 1464–1475 (2021)
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Journal Auto-deconvolution and molecular networking of gas chromatography–mass spectrometry data.
Nature Biotechnology 39, 169–173 (2021)
2020
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Journal Proceedings of the EuBIC-MS 2020 Developers' Meeting.
EuPA Open Proteomics 24, 1–6 (2020)
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Preprint Universal MS/MS visualization and retrieval with the Metabolomics Spectrum Resolver web service.
bioRxiv (2020)
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Book Identification of epitope-specific T cells in T-cell receptor repertoires.
Bioinformatics for Cancer Immunotherapy 2120, 183–195 (2020)
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Journal MESSAR: Automated recommendation of metabolite substructures from tandem mass spectra.
PLOS ONE 15, e0226770 (2020)
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Journal spectrum_utils: A Python package for mass spectrometry data processing and visualization.
Analytical Chemistry 92, 659–661 (2020)
2019
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Journal Detection of enriched T cell epitope specificity in full T cell receptor sequence repertoires.
Frontiers in Immunology 10, 2820 (2019)
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Journal Mining the enriched subgraphs for specific vertices in a biological graph.
IEEE/ACM Transactions on Computational Biology and Bioinformatics 16, 1496–1507 (2019)
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Journal 2018 YPIC Challenge: A case study in characterizing an unknown protein sample.
Journal of Proteome Research 18, 3936–3943 (2019)
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Journal Extremely fast and accurate open modification spectral library searching of high-resolution mass spectra using feature hashing and graphics processing units.
Journal of Proteome Research 18, 3792–3799 (2019)
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Journal Proceedings of the EuBIC Winter School 2019.
EuPA Open Proteomics 22–23, 4–7 (2019)
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Journal Using expert driven machine learning to enhance dynamic metabolomics data analysis.
Metabolites 9, 54 (2019)
2018
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Journal Fast open modification spectral library searching through approximate nearest neighbor indexing.
Journal of Proteome Research 17, 3463–3474 (2018)
"Rising Star in Proteomics and Metabolomics" awarded by the Journal of Proteome Research
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Journal Proceedings of the EuBIC Developer's Meeting 2018.
Journal of Proteomics 187, 25–27 (2018)
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Journal Grasping frequent subgraph mining for bioinformatics applications.
BioData Mining 11 (2018)
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Journal Quality control in mass spectrometry-based proteomics.
Mass Spectrometry Reviews 37, 697–711 (2018)
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Journal On the feasibility of mining CD8+ T-cell receptor patterns underlying immunogenic peptide recognition.
Immunogenetics 70, 159–168 (2018)
2017
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Journal Proteomics Standards Initiative: Fifteen years of progress and future work.
Journal of Proteome Research 16, 4288–4298 (2017)
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Journal A community proposal to integrate proteomics activities in ELIXIR [version 1; referees: 2 approved].
F1000Research 6, 875 (2017)
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Journal The Human Proteome Organization–Proteomics Standards Initiative Quality Control working group: Making quality control more accessible for biological mass spectrometry.
Analytical Chemistry 89, 4474–4479 (2017)
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Thesis Computational solutions for quality control of mass spectrometry-based proteomics.
Universiteit Antwerpen (2017)
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Journal Computational quality control tools for mass spectrometry proteomics.
PROTEOMICS 17, 1600159 (2017)
2016
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Journal Designing biomedical proteomics experiments: State-of-the-art and future perspectives.
Expert Review of Proteomics 13, 495–511 (2016)
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Journal Unsupervised quality assessment of mass spectrometry proteomics experiments by multivariate quality control metrics.
Journal of Proteome Research 15, 1300–1307 (2016)
2015
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Proceeding Discovery of significantly enriched subgraphs associated with selected vertices in a single graph.
Proceedings of the 14th International Workshop on Data Mining in Bioinformatics - BIOKDD '15 (2015)
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Journal iMonDB: Mass spectrometry quality control through instrument monitoring.
Journal of Proteome Research 14, 2360–2366 (2015)
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Journal A primer to frequent itemset mining for bioinformatics.
Briefings in Bioinformatics 16, 216–231 (2015)
2014
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Journal Efficient reduction of candidate matches in peptide spectrum library searching using the top k most intense peaks.
Journal of Proteome Research 13, 4175–4183 (2014)
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Journal qcML: An exchange format for quality control metrics from mass spectrometry experiments.
Molecular & Cellular Proteomics 13, 1905–1913 (2014)
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Journal jqcML: An open-source Java API for mass spectrometry quality control data in the qcML format.
Journal of Proteome Research 13, 3484–3487 (2014)
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Journal Machine learning applications in proteomics research: How the past can boost the future.
PROTEOMICS 14, 353–366 (2014)
Presentations
2022
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Invited A learned embedding for efficient joint analysis of millions of mass spectra.
Best of US HUPO 2022 (May 3, 2022)
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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)
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Oral A learned embedding for efficient joint analysis of millions of mass spectra.
US HUPO 2022, Charleston, SC, USA (March 1, 2022)
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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
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Poster Repository scale propagated spectral library of suspects for untargeted metabolomics.
ASMS annual conference, Philadelphia, PA, USA (November 2, 2021)
2020
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Oral Repository-scale propagated spectral library of suspects.
SoCal Science @Home Lollapalooza (December 1, 2020)
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Oral Deep neural network embedding for efficient repository-scale analysis of hundreds of millions of mass spectra.
ASMS 2020 Reboot (June 8, 2020)
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Oral Identifying millions of protein modifications using GPU-powered approximate nearest neighbor searching.
GPU Technology Conference (March 26, 2020)
2019
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Poster A learned embedding for efficient joint analysis of millions of mass spectra.
Machine Learning in Computational Biology, Vancouver, BC, Canada (December 14, 2019)
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Poster ANN-SoLo: Extremely fast and accurate open modification spectral library searching.
ASMS annual conference, Atlanta, GA, USA (June 3, 2019)
2018
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Poster Fast open modification spectral library searching through approximate nearest neighbor indexing.
Department of Genome Sciences retreat, Leavenworth, WA, USA (September 17, 2018)
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Oral Fast open modification spectral library searching through approximate nearest neighbor indexing.
Cascadia Proteomics Symposium, Seattle, WA, USA (July 23, 2018)
2017
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Poster Mass spectrometry proteomics: Ready for the deep learning (r)evolution?
ASMS annual conference, Indianapolis, IN, USA (June 8, 2017)
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Poster Towards the smart lab: A comprehensive approach to mass spectrometry quality control.
ASMS annual conference, Indianapolis, IN, USA (June 8, 2017)
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Invited Shedding light on complex mass spectrometry proteomics processes through advanced data mining.
Faculty of Science Research Day, Antwerp, Belgium (January 13, 2017)
2016
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Oral Git: How version control can power your research.
Biomina Lunch Talks, Antwerp, Belgium (June 24, 2016)
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Oral Optimized open modification spectral library searching using approximate nearest neighbor techniques.
ASMS annual conference, San Antonio, TX, USA (June 9, 2016)
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Poster Automatic quality assessment of mass spectrometry experiments by multivariate quality control metrics.
ASMS annual conference, San Antonio, TX, USA (June 9, 2016)
2015
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Oral Approaches for mass spectrometry quality control.
Biomina Research Day, Antwerp, Belgium (December 9, 2015)
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Oral Analysis of mass spectrometry quality control metrics.
Benelux Bioinformatics Conference, Antwerp, Belgium (December 7, 2015)
Outstanding oral presentation award
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Oral Precursor-free and fast spectral library search using approximate nearest neighbor techniques.
Benelux Bioinformatics Conference Student Council Symposium, Antwerp, Belgium (December 6, 2015)
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Poster Mass spectrometry quality control: Instrument monitoring and pattern mining insights.
ASMS annual conference, St. Louis, MO, USA (June 2, 2015)
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Software iMonDB: Mass spectrometry instrument monitoring for quality control.
Methods and tools for intra- and inter-experiment LC MS performance tracking workshop, ASMS annual conference, St. Louis, MO, USA (June 1, 2015)
2014
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Poster A comprehensive approach to mass spectrometry quality control.
Two-day symposium of the Belgian Proteomics Association, Brussels, Belgium (December 18, 2014)
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Oral Pattern mining of mass spectrometry quality control data.
Benelux Bioinformatics Conference, Luxembourg, Luxembourg (December 9, 2014)
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Poster Pattern mining of mass spectrometry quality control data.
European Conference on Computational Biology, Strasbourg, France (September 7, 2014)
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Poster Mining mass spectrometry quality control data.
ASMS annual conference, Baltimore, MD, USA (June 16, 2014)
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Oral Collecting and mining mass spectrometry quality control data.
Biomina Research Day, Antwerp, Belgium (February 20, 2014)
2013
Selected software
See also GitHub.

- GLEAMS
- Siamese deep neural network to embed mass spectra into a latent space.

- ANN-SoLo
- Fast and sensitive GPU-powered open modification spectral library searching.

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

- spectrum_utils
- Python package for efficient mass spectrum processing and visualization.