Trapped Ion Mobility-Assisted Sequencing and Analysis of Protein Ions

The sequencing of intact proteins within a mass spectrometer enables the profiling of post-translational modification (PTM) crosstalk but is frequently hindered by convoluted spectra and the fact that tandem mass spectrometry (MS/MS) techniques often generate poor sequence coverages when applied to protein ions. Ion mobility spectrometry is a promising tool to overcome the complexity of these spectra by separating ions by their mass- and size-to-charge ratios. Here, we discuss the development of an activation method that when paired with trapped ion mobility spectrometry deconvolutes MS/MS spectra and improves the sequence information provided by intact protein focused workflows. Furthermore, we demonstrate the isolation and fragmentation of mobility separated product ions with the downstream quadrupole and collisional cell. This second activation step improves sequence coverage because many of the labile bonds have been depleted during the first dissociation and subsequent dissociation events are more evenly distributed throughout the product ion backbone. When these two activation steps are combined this technique generates 92% of the sequence coverage of the most effective MS/MS technique, but it accomplishes this feat in a fifth of the time and can be facilely integrated with liquid chromatographic separations. Lastly, we demonstrate that this activation technique can be utilized to elucidate the conformation of protein ions.