Mass spectrometry integrates protein design into structural biology method development

Abstract Recent advances in machine learning (ML) have transformed protein science, enabling engineering and de novo design of artificial proteins with novel structures and functions. However, experimental analysis of key design features, such as oligomerization, folding, ligand binding, and dynamic conformational changes, remains critical. Here, we outline how mass spectrometry (MS) complements protein design through its ability to corroborate a wide range of design objectives. Furthermore, engineered proteins have become valuable tools for exploring the use of MS in detecting structural features, charge effects, and weak interactions by serving as testbeds for method development. Integrating ML and native MS thus creates a feedback loop: new designs challenge analytical techniques, while improved methods provide richer data to guide and improve future predictions. This synergy is vital for expanding the capabilities of protein engineering, including toward applications in synthetic biology and artificial protocell development.