Training of computational proteomics researchers

What is PROTrEIN?

PROTrEIN is a European Innovative Training Network composed of 11 beneficiaries, and 6 partner organizations, from the academic and non-academic sectors (including two SMEs and two large companies).

The network’s mission is to train a new generation of computational proteomics researchers by providing them an inter-sectoral and interdisciplinary set of skills to tackle the main challenges in the field and improve their future employability.

The project

Mass spectrometry-based proteomics is one of the most powerful technologies for studying the cellular proteome, protein interactions, and post-translational modifications. Although several proteomics workflows are well-established methods, the field is fast evolving with new acquisition approaches and generating of high-content data structures. This evolution has expanded the number of applications, and mass spectrometry-based proteomics has become one of the principal platforms in the multi-omics universe. However, many of these developments require the assistance of machine learning approaches to predict peptide properties and to optimize the acquisition of proteomics datasets. Similarly, these new applications often require the development of new processing algorithms to query and interpret raw mass spectrometry data, and therefore reveal hidden proteoforms, interactions, and protein modifications.

Finally, the implementation of new experimental possibilities also requires the development of interactive and highly-visual tools for the integration and representation of proteomics data with other omics datasets. Addressing these different needs is crucial to use proteomics at its full potential and thus deliver key contributions in our understanding of biological processes to support the health sector with valuable information.

Scientific & Technical Objectives

PROTrEIN has developed a highly multi-and inter-disciplinary translational research and training network that will exploit the integrated analysis of several state-of-the-art technologies to achieve these ambitious goals:

We need a new generation of researchers that can delve into the complexity of the computational proteomics field. PROTrEIN aims to nurture this new generation of computational proteomics scientists by training them on the mastering of i) the mass spectrometry raw data nature, structure and information content, ii) mass spectrometry acquisition methods, iii) algorithms, gamification and machine learning tools, iv) data integration and visualization, v) science communication, vi) data management and vii) research integrity and innovation (RRI).

To successfully achieve the goal described above, we have designed a comprehensive research program around the development of new proteomics predictors using machine and deep learning technologies, new raw data processing algorithms that enable new proteomics applications, and omics data integration and visualization.

PROTrEIN is defined in seven work packages (WPs)

Comprising three scientific work packages that cover the main research program, to which all 15 individual research projects contribute:

WP1 Coordination; WP2 Novel machine learning predictors; WP3 New algorithms for data processing; WP4 Integration and visualization; WP5 Translation and Exploitation; WP6 Dissemination and Communication; WP7 Training.