Join us for the EuBIC-MS Winter School 2026 – a biennial meeting focused on computational approaches for mass spectrometry–based omics. The event brings together leading scientists and early-career researchers for keynote lectures, hands-on workshops, and networking opportunities, fostering collaboration and knowledge exchange within the MS bioinformatics community.
This year, we will cover a wide range of topics at the intersection of mass spectrometry and computational biology, including single-cell proteomics, immunopeptidomics, metabolomics, and multi-omics data integration. Key discussions will focus on developing advanced workflows, AI-driven bioinformatics, and innovative computational tools to enhance the scalability, reproducibility, and interpretability of proteomics and metabolomics data across diverse biological applications.
Follow us on Bluesky (@eubic-ms.org) or LinkedIn (EuBIC-MS) for the latest updates and announcements.
The EuBIC-MS Winter School in a nutshell
The EuBIC-MS Winter School is a biennial conference dedicated to computational approaches for mass spectrometry–based omics, bringing together researchers, developers, and practitioners from across Europe and beyond. The 2026 edition will be held from 19–23 January 2026 in Harrachov, Czech Republic, at the OREA Resort Sklář.
The program begins with an educational day focused on workshops and training sessions covering established computational MS tools and workflows. The following days feature keynote lectures from internationally renowned scientists, alongside practical workshops addressing key topics such as identification, quantification, result interpretation, and integration of MS data. This structure ensures a balanced mix of theoretical insight and hands-on learning, fostering both knowledge transfer and practical skill development.
The EuBIC-MS Winter School provides a collaborative environment that encourages networking and the exchange of ideas across the mass spectrometry bioinformatics community.
Conference program
Educational day
The Winter School opens with a full day dedicated to training and education. Participants will be introduced to established computational mass spectrometry tools and workflows through tutorials and guided sessions. This day is designed to provide a solid foundation for early-career researchers while also offering opportunities for more experienced participants to deepen their knowledge.
| Session | Subject | Trainers |
|---|---|---|
| Parallel session 1 (4.5 hours) | Introduction to computational proteomics, OpenMS, and pyOpenMS | OpenMS team |
| Intro to computational metabolomics, and mzMine | mzMine team | |
| Parallel session 2 (2 hours) | Games in science education | Karel Berka |
| Machine learning in proteomics, and ProteomicsML | Ralf Gabriels |
Expert keynotes
Our keynote speakers span different career stages and represent diverse expertise from across Europe and beyond. Together, they will share new methods, applications, and perspectives shaping the future of computational mass spectrometry.
Armin Soleymaniniya
Wilhelm Group, Technical University of Munich, Germany
A computational journey into plant proteomics
Arthur Declercq
CompOmics Group, VIB – Ghent University, Belgium
AI-driven immunopeptide discovery with MS²Rescore and MHC-3PO
Claire Koenig
Olsen Group, University of Copenhagen, Denmark
Untangling kinase activity: From phosphosites to meaningful biology
Hannah Boekweg
Payne Lab, Brigham Young University (formerly), United States
Statistical methods designed for single-cell data that more accurately detects differentially abundant proteins
Jonas Scheid
Walz Group, University Hospital Tübingen (QBiC), Germany
Standardizing immunopeptidomics analyses at scale with nf-core
Karel Berka
Palacký University Olomouc, Czech Republic
Alphafoldology
Matthias Anagho-Mattanovich
Moritz Group, University of Copenhagen, Denmark
What stable-isotope labeling of metabolites teaches us about metabolism
Roman Bushuiev
Pluskal group, IOCB Prague and Czech Technical University, Czech Republic
Deciphering tandem mass spectra at scale with DreaMS
Samuel Wein
OpenMS, Tübingen, Germany
Scaling mass spectrometry: From peaks to platforms
Valdemaras Petrosius
Schoof group, Technical University of Denmark, Denmark
Exploring cellular heterogeneity with sensitivity tailored proteomics
Hands-on workshops
Join hands-on workshops led by keynote speakers and invited experts to gain practical experience with cutting-edge computational tools and workflows. These sessions are designed to complement the keynote lectures by giving you the opportunity to apply methods directly, explore new approaches, and strengthen your technical skills. The workshops provide an interactive setting where you can learn from experienced developers, exchange ideas with peers, and bring home knowledge that can be applied in your own research.
| Session | Trainers | Title |
|---|---|---|
| Tuesday | Karel Berka | Alphafoldology |
| BSI / Peaks (sponsored) | PEAKS Proteomics Solutions with High Sensitivity, Accuracy, and Speed | |
| Tesorai (sponsored) | Improving MS Search Engine Performance and Biological Interpretation with AI-Driven Tools | |
| Wednesday | Claire Koenig | Paleoproteomics |
| Roman Bushuiev | DreaMS & MassSpecGym | |
| Matthias Anagho-Mattanovich | m/z to mp3: listening to analytical instruments with ms_music | |
| Thursday | Jonas Scheid | Immunopeptidomics applications – From spectra to therapeutically relevant antigens |
| Armin Soleymaniniya | Hands-on rescoring of proteomics results with Oktoberfest |
Present your work with a poster or flash talk
Abstracts are submitted for poster presentations, with the option to apply for a flash talk to promote your poster. All submissions that meet our quality criteria and are relevant to the general audience of the event will be accepted for a poster presentation. For flash talks, the organizing committee will select a subset of abstracts based on the same criteria of quality and relevance. Abstract submission, flash talk applications, and EuPA Travel Grant applications are handled through the same online form.
Preliminary schedule
Note that the preliminary program will be adjusted as planning progresses.
About EuBIC-MS
The European Bioinformatics Community for Mass Spectrometry (EuBIC-MS) is an initiative of the European Proteomics Association (EuPA), founded in 2015 to advance bioinformatics for mass spectrometry-based omics. It provides an open and collaborative environment for researchers, developers, and users, aiming to improve tools, training, and resources. EuBIC-MS conferences alternate each year between a Winter School, focused on lectures and workshops, and a Developers Meeting, centered on hackathons and collaborative development.
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About the keynote speakers
Armin Soleymaniniya
Armin Soleymaniniya is a PhD candidate in the Associate Professorship of Computational Mass Spectrometry at the Technical University of Munich. His research centers on peptide identification, large-scale data integration and reuse, and providing proteomics data in an accessible and FAIR way. He is a leading developer of ProteomicsDB, with a focus on large-scale data integration and the development of cross-species features. In addition, he contributes to the Proteomes that Feed the World project, which applies proteomics to advance agricultural sustainability and food security. By combining predictive models, workflow automation, and open data infrastructures, his work enhances the scalability and reproducibility of proteomics analysis and supports new applications across species.
Arthur Declercq
Arthur Declercq is a postdoctoral researcher in the CompOmics group at Ghent University, where he recently completed his PhD in Health Sciences. With a background in biomedical sciences and a strong interest in immunology and bioinformatics, his research focuses on developing computational methods for immunopeptidomics. He has created algorithms to identify MHC-bound epitopes, which are central to advancing vaccine design for cancer and infectious diseases. He is the developer of TIMS²Rescore and received the 2023 PhD Innovation Café award from VOKA and UGent. By combining immunology with AI-driven bioinformatics, his work contributes to overcoming current challenges in vaccine development.
Claire Koenig
Claire Koenig is a postdoctoral researcher in the Olsen Group at the University of Copenhagen. With a background in analytical chemistry and mass spectrometry–based proteomics, her work focuses on developing streamlined and high-throughput workflows that expand the capabilities of proteomics. She has applied these methods across diverse fields, from palaeoproteomics to quantitative phosphoproteomics of human cell systems. Her current research centers on advancing phosphoproteomics to investigate cellular signaling and regulatory processes, with the aim of broadening the accessibility and impact of mass spectrometry technologies across biomedical research.
Hannah Boekweg
Hannah Boekweg is a researcher specializing in computational methods for single-cell proteomics. She recently completed her doctorate in bioinformatics, where she developed new algorithms for protein quantification and statistical models tailored to the unique challenges of single-cell data. Her work also addresses study design, including approaches for determining sample size requirements in time-course trajectory analyses. By advancing computational frameworks for single-cell proteomics, she contributes to improving the accuracy, interpretability, and scalability of this rapidly emerging field.
Jonas Scheid
Jonas Scheid is a PhD candidate at the University Hospital Tübingen, working within the Quantitative Biology Center (QBiC). With a background in biology and bioinformatics from the University of Tübingen, his research focuses on computational immunology and the development of streamlined workflows for immunopeptidomics. He is a lead contributor to MHCquant2, a pipeline that integrates and optimizes analysis steps to refine tumor antigen discovery. By advancing reproducibility and scalability in immunopeptidomics, his work supports the identification of clinically relevant antigens for next-generation cancer immunotherapies.
Karel Berka
Karel Berka is Professor of Biomolecular Chemistry and Structural Biology at Palacký University Olomouc, where he leads the Chemical Datalab team in the Department of Physical Chemistry. His research combines theoretical chemistry and bioinformatics to study proteins and membranes, with a focus on ligand binding and molecular access routes in protein structures. He has pioneered resources such as the MolMeDB database for molecule–membrane interactions, the MOLE program for channel and tunnel computation, and ChannelsDB for mapping access routes in proteins. He also serves as Vice-Head of ELIXIR-CZ, the Czech national life science infrastructure, where he is responsible for structural bioinformatics.
Matthias Anagho-Mattanovich
Matthias Anagho-Mattanovich is a postdoctoral researcher at the University of Copenhagen. He studied biotechnology at BOKU in Vienna, with part of his Master’s completed at INSA in Toulouse, before earning a PhD at the Novo Nordisk Foundation Center for Biosustainability at DTU. His doctoral work focused on automation for multi-omics data generation and analysis. He now works with Thomas Moritz at the NNF Center for Basic Metabolic Research, where he develops metabolomics workflows and systems-level approaches to advance the understanding of metabolism and disease.
Roman Bushuiev
Roman Bushuiev is a PhD candidate at IOCB Prague and the Czech Technical University. His research focuses on applying machine learning to natural product discovery, with a particular emphasis on interpreting small-molecule mass spectrometry data. He leads the development of the DreaMS and MassSpecGym projects, which advance benchmarking and data analysis in this area. In addition, he develops machine learning approaches for protein science, including applications in protein engineering and function prediction, bridging computational innovation with biological discovery.
Samuel Wein
Dr. Sam Wein is a fellow at the University of Tübingen where his primary research interests are computational mass spectrometry (MS) (especially of oligonucleotides), as well as development of standards for storing and conveying MS experiments. Sam is a core developer of the OpenMS project and serves as CEO of OpenMS inc, a company focused on advancing open‑source MS software infrastructure and analytics solutions. He earned his PhD from the University of Pennsylvania in biochemistry and molecular biophysics in 2019 developing a full pipeline from cells to data analysis for RNA. Sam has held a deep interest in open-source philosophy ever since being exposed to Linux in his teen years, and is seeking to expand the reach of open-source software in the sciences. Sam currently lives in Oldenburg, Germany with his wife Amanda and their cat Athena. When not coding, analyzing data, or responding to emails, Sam enjoys brewing beer, long bike rides through the forest, and traveling.
Valdemaras Petrosius
Valdemaras Petrosius is an Assistant Professor in the group of Erwin M. Schoof at the Technical University of Denmark. His research focuses on developing highly sensitive mass spectrometry workflows for low-input and single-cell proteomics, enabling the study of rare cell populations with exceptional depth and accuracy. These approaches are applied to key biological questions such as stem cell dynamics and cancer stem cell resistance. In parallel, he develops computational strategies to ensure robust, scalable, and reproducible data analysis. His work aims to uncover how cellular heterogeneity shapes health and disease.
Important dates & deadlines
Registration
| Registration opens | 15 October 2025 |
| Early bird registration closes | |
| General registration closes | 12 January 2026 |
Abstracts
| Abstract submission opens | 15 October 2025 |
| Abstract submission closes | 12 December 2025 |
Event
| Winter School | 19-23 January 2025 |
Venue and travel
OREA Resort Sklář
Harrachov 520
512 46 Harrachov
Czechia
We will provide shuttle bus transfers between Prague Central Station, Prague Airport, and OREA Resort Sklář in Harrachov at the start and end of the Winter School. Shuttle buses operate only at the announced dates and times; please plan to arrive at the pick-up point in good time, as the buses cannot wait for late arrivals. Exact meeting points and practical instructions will be shared closer to the event by email and via the Winter School Slack workspace.
Harrachov is also easily reachable by public transport, with frequent, fast, and affordable bus connections to/from Prague. If you prefer to travel independently, or if you miss the shuttle, we recommend checking up-to-date schedules and route options via IDOS: https://idos.cz/en/vlakyautobusymhdvse/spojeni/?f=Praha&fc=1&t=Harrachov;%20Jablonec%20nad%20Nisou&tc=1.
Accommodation
Accommodation is available at the conference hotel at a reduced rate for Winter School participants. The rate is €163 per night for a single room (1 person) and €171 per night for a double room (2 persons). Rooms are limited and will be allocated on a first-come, first-served basis, and the hotel may fill quickly as it is a popular ski resort. The booking URL and reservation code will be communicated after registration.
Travel grants
EuPA-sponsored travel grants are available to support attendees with limited access to funds. You can apply directly through the abstract submission form (personal statement required). In addition, many national proteomics societies offer independent travel-grant schemes—please consult your society for eligibility and deadlines.
Cancellation and refund policy
Cancellations must be submitted in writing by email to winterschool@eubic-ms.org. They will only be accepted if received at least 14 days prior to the first day of the event (the email date will be considered the cancellation date). Cancellations received after this deadline, as well as no-shows, are not eligible for a refund, and the full registration fee remains due. For all cancellations, the registration fee will be reimbursed only partially, after deduction of a handling fee. The exact amount of this fee depends on the actual costs of processing the reversal.
The organizers reserve the right to cancel all or parts of the event at short notice. In such cases, all paid fees will be refunded in full, minus an administrative fee of 50 EUR.
Organizational & legal information
The Czech Society for Mass Spectrometry (CSMS) serves as the local and financial organizer of the Winter School. Registration fees are received by CSMS. All payments are processed via secure card checkout; the details below are provided for administrative use.
CSMS — Česká společnost pro hmotnostní spektrometrii (Czech Society for Mass Spectrometry)
Přírodovědecká fakulta, Univerzita Palackého v Olomouci
17. listopadu 1192/12
771 46 Olomouc 9
Czech Republic
IČ: 22858938
Číslo účtu: 240033266 / 0300
IBAN: CZ17 0300 0000 0002 4003 3266
SWIFT/BIC: CEKOCZPP
EuBIC-MS coordinates the scientific program and community activities. It is an initiative of the European Proteomics Association (EuPA).
European Proteomics Association e. V.
c/o Prof. Stefan Tenzer
Universitätsmedizin Mainz
Institut für Immunologie, Gebäude 308A
Langenbeckstr. 1
D-55131 Mainz
Germany
Association register: VR 7217
Registration court: Dortmund District Court
Registration
The following registration fees apply:
| Early bird registration | General registration | |
| Academic | €500 | €600 |
| Industry | €700 | €800 |
The registration fee includes:
- Access to all main Winter School sessions (keynotes, workshops, poster session, social event, …)
- Receipt of all main conference materials
- Coffee breaks and lunches on five conference days
The registration fee does not include:
- Travel costs
- Hotel accommodation
- Breakfast
- Dinner
- Additional social activities
Capacity is limited to 200 participants, and places are allocated on a first-come, first-served basis.
After registering, do not forget to book your accommodation with the provided booking code, and to submit your poster abstract.
Registration is closed.
Organizational committee
Bart Van Puyvelde
Julian Uszkoreit
Karolína Kryštofová
Louise Buur
Ralf Gabriels
Veit Schwämmle
Would you like to be involved in the organization? Become a EuBIC-MS member and join the #2026-winter-school channel in our Slack workspace.
Contact
Questions about the Winter School? Reach out to us at winterschool@eubic-ms.org.