H2020 EPIC-XS Project: The European Proteomics Infrastructure Consortium provides access

Since the start of the project, EPIC-XS provided access to 240 projects involving 221 users, of which 102 were women and 119 were men. EPIC-XS users were mostly academic, but the consortium also worked with non-academic stakeholders, primarily to inform them about the possibilities of newly developed high-end proteomics methodologies, but also to participate in EPIC-XS TNA opportunities. Hands-on training helped researchers develop best-practice workflows and disseminate proteomics data in publicly available databases, thus expanding the knowledge of both experienced scientists and those new to the field of proteomics. Standard operating procedures and new protocols were rapidly exchanged between access sites, expanding and strengthening the services that can be offered across Europe. Transnational access was provided to institutions in 33 different countries, and in total, this access has already resulted in the publication of 44 articles from the user projects alone.

Joint Research Activities EPIC-XS featured four Joint Research Activities (JRAs) that were interactive efforts among EPIC-XS partners and have resulted in innovative new proteomic technologies. Proteomics research is evolving at an astonishing pace. Tremendous leaps forward have been made in terms of sensitivity, dynamic range, comprehensiveness, robustness, and costs (in time and money). These steps have enabled proteomics to impact both fundamental and translational research, benefiting humanity. Proteomics can now be used to investigate the proteome of single cells by discovering new cells and cellular responses, analyze hundreds of thousands of clinical samples for diagnostic protein markers of health and disease, map the spatiotemporal behavior of proteins in cells and tissues, and how they functionally interact with each other.

EPIC-XS joint research activities have pioneered many of these proteomic technologies and contributed to the translation of these technologies to the clinic and to the broader life science research communities. EPIC-XS researchers have been instrumental in making these advances in proteomic methods possible. A new frontier in proteomics comes from more protein-centric (top-down) approaches, which complement the already more routine peptide-centric (bottom-up) approaches. Protein-centric approaches are important for the detection of "proteoforms," a term that designates all the shapes that proteins, linked to a gene, can have in our cells or subcellular organelles or tissues. Although our DNA only contains about 20,000 genes, recent work on the proteoform conducted by other EPIC-XS partners has revealed that the number of proteoforms can easily exceed several million.

To understand true regulation in molecular biology, we need tools that allow us to dissect the functional roles not only of selected genes, but of every proteoform, visualizing its structure and function, localization, and interactions. This is a very ambitious goal, but essential for making impactful contributions to our understanding of biology. Several partners in the EPIC-XS consortium have implemented structural proteomics approaches in their work, deriving structural information about proteins that can be directly related to cryoEM, microscopy, and computational data. The obtained (cryoEM) or predicted (AI using Alphafold) structures are validated by emerging proteomic technologies such as limited proteolysis (LipMS), crosslinking MS (XL-MS), and hydrogen-deuterium exchange MS, and these methods are now frequently exploited through biomolecular, biotechnological, and biomedical applications, aiding the development of, for example, new drugs.

The equipment used to obtain proteomics-based information is expensive, and capacity is often a limiting factor, as is the expertise to analyze the data. AI technologies have also entered the field of proteomics and have already contributed greatly to improving the analysis and biological interpretation of the vast amount of data generated. To fully benefit from the rapid expansion of proteomics research tools, biomedical and biological researchers need access and support.