ProtAIomics is a Horizon Europe MSCA Doctoral Network that brings together 15 beneficiaries and 9 associated partners across academia, biotech and big-pharma to train 16 doctoral candidates at the interface of artificial intelligence and mass-spectrometry proteomics. By combining expertise in machine learning, structural biology and systems modelling, the network tackles the entire proteomics value chain—from data acquisition to actionable biomedical insights—while equipping a new generation of researchers with interdisciplinary, industry-relevant skills.