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Pre-Congress Workshops

Sunday, October 20, 2024 - 8:30-14:15

To attend our pre-congress training courses, you'll need to book them separately. Your booking includes access to all available courses.
Just click here to sign up for your chosen course.

Chemical Proteomics and Drug Discovery

Ben Collins
(Queen’s University Belfast), Madeline Kavanagh (Leiden University)
(co-organized by HUPO Education and Training Committee)

Background and rationale:
Proteomics is becoming a key technology in the context of drug discovery research, and we expect its importance to continue to grow. This is driven by (i) emerging drug modalities where large-scale protein measurements are directly relevant (e.g. targeted degraders and induced proximity generally, covalent inhibitors, antibody drug conjugates, etc), as well as (ii) general improvements in proteomics technologies and data quality. Drug discovery companies and CROs are active in this space but links to academic scientists are weak and HUPO activity in this key area is currently limited. This lack of activity presents an opportunity for a HUPO initiative on ‘Chemoproteomics and Drug Discovery (CPDD)’. With this workshop we aim to familiarize HUPO members with current activity and opportunities in this area, and to assess the feasibility of launching HUPO initiative in this key space.

Chemical Proteomics Strategies in Drug Discovery – Mikhail Savitski (EMBL)
  • The goal here will be to survey the space of technologies and applications used in chemical proteomics and drug discovery.
The view from CRO land – How pharma/biotech uses proteomics – Lukas Reiter (Biognosys)
  • Overview of how pharma and biotech actually use proteomics technologies and the value they place on proteomics to support discovery/development workflows.
Proteomics driven drug discovery in a startup company – Lindsay Pino (Talus Bio)
  • How can a platform-based startup in early-stage drug discovery leverage unique proteomics technologies to drive their model?
Panel Discussion (speakers and chairs)
  • a) How can we connect proteomics researchers (e.g. HUPO members) to academic/industrial researchers in the chemical biology and early-stage drug discovery space?
  • b) Does HUPO need a specific initiative focused on Chemical Proteomics and Drug Discovery? – If so, what activities would be the highest value activities?


How to get the most out of your proteomics core facility, a Core 4 Life initiative

Dr. Dominic Helm
(Proteomics Core facility, German Cancer Research Center (DKFZ), Heidelberg, Germany), Dr. Mariette Matondo (Pasteur Proteomics Facility, Institut Pasteur, Paris, France)

Core facilities have emerged as key assets for scientific research infrastructures by centralizing expertise and technology and thus providing support in specialized and technology driven research fields, for example proteomics. These expertise units enable research labs to have access to contemporary proteomics platforms and truly advance research.

This session aims to provide information on how to run a (mass spectrometry) proteomics core facility, and how to run proteomics workflows in a robust and reliable way. Which key aspects need to be tackled in order to maximize the success rate of bringing different projects to completion. And as a core facility, what do you need from the user to safeguard the overall analysis quality.

To assure the reliable and reproducible generation of mass spectrometry-generated proteomics data, standardized quality control procedures are essential. Ideally, these procedures are implemented throughout different proteomics core facilities and research groups to enable inter-laboratory harmonization in defining optimal performance conditions of both LC and MS infrastructure. In this session we will elaborate on some QC initiatives across core facilities to enhance data comparability and reliability.

How to run your proteomics core facility?
Speaker: Dr. Simon Devos
, head of the VIB Proteomics Core, Flemish Institute of Biotechnology (VIB), Ghent, Belgium
  • What impact do core facilities have on proteomics research, and what can you do to maximize the success of the project outcome, either as a customer or as a core facility employee
How to control sample and instrument quality?
Speaker: Dr. Eduard Sabidó
, head of the Proteomics Unit, Center for Genomic Regulation (CRG), Barcelona, Spain
  • How can you monitor, in a transparent way, the performance of your LC-MS infrastructure, and keep track of the quality of the samples that are being analyzed?
How to choose the best method for sample preparation, LC-MS analysis, data analysis and data management?
Speaker: An Staes
, VIB Proteomics Core, Flemish Institute of Biotechnology (VIB), Ghent, Belgium; Paolo Nanni, Functional Genomics Center Zurich (FGCZ), Zurich, Switzerland
  • There are numerous ways to tackle your needs for sample preparation, LC-MS analysis, and data analysis, and the field is constantly evolving. How can you choose the best method for your project, and how can you benchmark new methods?
What can you do to improve the performance of your core facility?
Speaker: Mandy Rettel, Proteomics Core Facility, EMBL, Heidelberg, Germany; Anna Shevchenko, Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
  • Interactive sessions to shed light on how to boost the facility’s performance.


Delving into biodiversity’s depths: integrating new model organisms and unravelling the mysteries of unknown proteins

Fabrice Bertile (University of Strasbourg/CNRS, France), Susana Cristobal (Linköping University, Sweden)

Short description
In today’s post-genomic era, it is crucial to reconsider the concept of model organisms and unravel the functions of uncharacterized proteins. Beyond the so-called 'standard model organisms’ (from lab rodents to E. coli), broader inclusion is now imperative to bring new scientific insights by exploring novel organisms/models (from complex microbial communities to holobionts). The pursuit of uncharacterized proteins in relevant models opens doors to a vast sea of unknowns, essential for a comprehensive understanding of biological processes across biodiversity. By fostering interdisciplinary collaborations among the fields of biology, advanced molecular sciences and (meta)omics, we can collectively adopt new models, elucidate their molecular functioning and uncover fundamental mechanisms. Multi-disciplinary approaches, with proteomics and proteogenomics at the forefront, can enhance the functional characterization of proteins with limited structural and functional knowledge. By convening scientists with diverse expertise and backgrounds, this symposium will make significant contributions to urgent topics spanning human health, environmental perturbations, and biodiversity conservation management.

Have you ever dreamed of uncovering the function of those enigmatic unknown proteins that consistently appear in your list of abundant and differentially regulated proteins? Have you ever dreamed of uncovering new fundamental knowledge? How can we collectively address these challenges? These are the pivotal questions our community is eager to discuss, offering collective insights, sharing results, and making collaborative contributions. This symposium will foster collaborative studies among diverse scientific communities (omics, (eco)physiology, ecotoxicology, evolutionary biology, bioinformatics) thus enriching the understanding of biological systems and molecular pathways through comparative biology - a transformative leap that will undoubtedly benefit human and environmental health.

Ecotoxicology in an omics world – Sabine Matallana-Surget (University of Stirling, UK)
Holobiont models: improving our understanding of biological complexity – Jean Armengaud (JOLIOT Institute/CEA, France)
Ghost Proteins: An Analogy to Novel Model Organisms for Deciphering Protein Functions – Tristan Cardon (Université de Lille/INSERM, France)
Comparative (multi)omics approaches have the potential to bring new knowledge – Fabrice Bertile (University of Strasbourg/CNRS, France)


Blood proteomics – lost in translation

Jochen Schwenk and Vera Ignjatovic

The what:
Our session focuses on the bridge between clinical and research-centric proteomics, with state-of-the-art talks highlighting the importance of the samples and the technological innovation in use. Rationale (the why):

  • Sample source and type are an afterthought. This is critical, particularly as proteomics publications reach a broader user base (e.g., increasingly published in non-proteomics journals).
  • Innovations in blood collection (e.g., microsampling) and how these can be applied in proteomics studies.
  • Blood proteomics publications often misjudge the impact of sample collections and processing. This makes interpretation, validation, and translations almost impossible, especially for existing datasets.
  • What key factors and best practices should be considered when doing blood proteomics?
Setting the stage – Jochen Schwenk
Know your sample, know your bias – TBA
The clinical lab perspective – Steven Bruzek
Sample integrity – Vincent Albrecht
Standardization for translation – Markus Ralser
Q&A – Jochen Schwenk & Vera Ignjatovic
Call to arms – standardization – Vera Ignjatovic