Atomic-level protein structure characterization by tandem-trapped ion mobility spectrometry/tandem-mass spectrometry coupled with UV photodissociation

The complexity of the proteome at all levels of protein structure and dynamics renders the systematic identification of how protein modifications alter protein-protein interaction networks and cause disease a formidable, unsolved challenge. Mass spectrometry-methods enable the detection of protein modifications causing disease on a proteome-wide scale but do not provide direct structural information to reveal the molecular origins of disease-causing events. Here, we demonstrate that (i) ultraviolet photodissociation coupled with a tandem-trapped ion mobility spectrometer/tandem-mass spectrometer dissociates the protein ubiquitin into fragments with native-like structures and (ii) the collision cross-sections of these native-like fragments sufficiently constrain the ubiquitin structure to reveal its atomic-level structure using computational approaches. Because of the throughput, sensitivity, and dynamic range of mass spectrometry, our approach is expected to enable the systematic discovery of how protein modifications alter protein structure, misregulate protein interaction networks, and cause disease at the molecular level and on a proteome-wide scale