Protocol for structural analysis of amyloid fibrils using hydrogen-deuterium exchange mass spectrometry

Amyloid fibrils are common in many diseases. Here, we present a protocol that uses α-synuclein fibrils, a Parkinson's disease hallmark, to demonstrate hydrogen-deuterium exchange (HDX) mass spectrometry (HDX-MS) for amyloid protein structural analysis. We describe steps for fibril preparation, quality assessment, HDX labeling, digestion, and mass spectrometry. We then detail procedures for peptide mapping and data interpretation. This protocol serves as a practical guide for new and experienced researchers to study insoluble protein aggregates with distinct conformations. For complete details on the use and execution of this protocol, please refer to Han et al.¹.