Wout Bittremieux
Postdoctoral researcher

Wout Bittremieux

Dorrestein Laboratory — University of California San Diego
ADReM Data Lab — University of Antwerp

University of California San Diego
Skaggs School of Pharmacy and Pharmaceutical Sciences
9500 Gilman Drive
La Jolla, CA 92093-0751
  • 0000-0002-3105-1359
  • wbittremieux AT health DOT ucsd DOT edu
  • first name DOT last name AT uantwerpen DOT be
  • PGP fingerprint: 083A D4DD D94E BAEB F2EF 31A8 E6EE 659B 9DA2 F90F (show full key)
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About me

I am a bioinformatics postdoctoral researcher at the Dorrestein Laboratory of the University of California San Diego and the ADReM Data Lab of the University of Antwerp.

My research deals with developing advanced machine learning methods to uncover novel knowledge from mass spectrometry-based metabolomics and proteomics data. Besides my main research focus on using deep learning to analyze mass spectrometry data I am interested in a wide variety of bioinformatics problems. An important part of my work deals with developing insights and computational approaches for quality control for biological mass spectrometry.

Curriculum vitae.

Publications

See also Google Scholar.

2021

  • Preprint Multi-omics profiling of Earth's biomes reveals that microbial and metabolite composition are shaped by the environment.   

    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

    bioRxiv (2021)

  • Preprint ppx: Programmatic access to proteomics data repositories.   

    William E. Fondrie, Wout Bittremieux, William S. Noble

    bioRxiv (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, in press (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)

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

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

    bioRxiv (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 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, bbaa318 (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)

  • Preprint Reference data based insights expand understanding of human metabolomes.   

    Julia M. Gauglitz, Wout Bittremieux, Candace L. Williams, Kelly C. Weldon, Morgan W. Panitchpakdi, Francesca Di Ottavio, Christine M. Aceves, Elizabeth Brown, Nicole C. Sikora, Alan K. Jarmusch, Cameron Martino, Anupriya Tripathi, Erfan Sayyari, Justin 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, Dominic S. Nguyen, 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 Protaso Veras, Thiago Mattar Cunha, Rene Donizeti Ribeiro Oliveira, Paulo Louzada-Junior, Robert H. Mills, Douglas Galasko, Parambir S. Dulai, Curt Wittenberg, David J. Gonzalez, 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

    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)

  • 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

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 annual conference, 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 annual conference, Indianapolis, IN, USA (June 8, 2017)

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

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

  • Oral 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 annual conference, San Antonio, TX, USA (June 9, 2016)

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

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

  • 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

  • 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 annual conference, 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.

ANN-SoLo
ANN-SoLo
Fast open modification spectral library searching using approximate nearest neighbor indexing.
iMonDB
iMonDB
Tool suite to automatically extract, store, manage, and visualize mass spectrometry instrument metrics for quality control.
jqcML
jqcML
Highly performant Java API for the qcML standard file format for mass spectrometry quality control data.
QC analysis
QC analysis
Machine learning workflow to detect low-quality mass spectrometry experiments for automated decision-making.