Pre-Congress Workshops

Chairs:
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.

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

Abstracts:
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.

Chairs:
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.

Audience
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.

Co-Chairs:
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?

Session Chairs: Cecilia Lindskog (Uppsala University, Sweden); Michael H. Roehrl (Beth Israel Deaconess Medical Center, Harvard Medical School, Boston)

Short description:
The introduction of the Pathology and Precision Medicine Pillar to the Human Proteome Project acknowledges the key roles that pathology and laboratory medicine play in the delivery of proteomics-driven biomarker discovery for clinically useful diagnostics and theranostics. It also recognizes the fundamental importance of new proteomic assays for advancing personalized precision medicine. Our pre-congress session with the subject “Proteomics for Precision Medicine” features speakers from pathology, medical oncology, the diagnostics industry, and therapeutic development. We hope to attract a broad audience with interest in applying proteomics to human health and medicine (physicians, basic and translational scientists, members from pharma/life science biotech).

Our session aims to broaden the reach and scope of HUPO to include and attract a growing number of physicians and scientists from healthcare into our proteomics community to advance medicine and to improve the lives of patients.

Chairs and Speakers:

HUPO has expanded its mission beyond human proteomics to embrace 'One Health Approaches', encompassing plants, food, nutrition, and the environment, thus welcoming all facets of proteome research. Plants represent the nutritional basis of virtually all life on earth and are essential for feeding an increasing human population while facing new challenges posed by climate change. Despite the increasing elucidation of crop genomes and transcriptomes, our understanding of crop proteomes remains very limited. To address this knowledge gap, we have launched a new initiative with far-reaching socio-economic relevance. The main goal of a new program called “The Proteomes that Feed the World” is to map the proteomes of all major tissues and organs of the 100 crop plants most important for human nutrition. This will create a Crop Proteome Atlas of high value to academia as well as the agricultural and food industries.

The proposed pre-congress session is structured with three main objectives in mind. First, it aims to introduce the Crop Proteome Atlas and its integration into ProteomicsDB to a wider audience within the proteomics community. Second, it seeks to gather valuable feedback from participants attending the session. Last, but not least, the session endeavors to explore opportunities for enhanced community engagement and collaboration.

Our 90-minute pre-congress session on "The Proteomes that Feed the World" will be led by the initiative's two speakers – one proteomics expert and one plant biologist. This session intends to engage a diverse audience profoundly interested in the application of proteomics to crop sciences. In line with the broadened scope of HUPO, our session aims to attract plant biologists, proteome scientists and bioinformatics experts, fostering collaboration and integration within the proteomics community.