Ion mobility spectrometry-mass spectrometry methods offer the potential to correlate protein tertiary and quaternary structures to variations in their amino acid sequences and post-translational modifications. Here, we apply our computational Structure Relaxation Approximation (SRA) method to elucidate detailed protein structures from measurements carried out on our tandem-trapped ion mobility spectrometry / mass spectrometry (TIMS/TIMS-MS) instrument. We developed the Structure Relaxation Approximation (SRA) method to quantitatively and predictively interpret ion mobility spectra in terms of the ion structure. The central idea of the SRA is to predict charge-state specific ion mobility spectra from an ensemble of solution structures. Hence, the more charge states and experimental conditions are probed by experiment and theory, the greater the confidence of the structural interpretation will be because chance agreement for all conditions and charge states becomes increasingly unlikely. Here, we discuss application of the SRA method to elucidate proteins structures from measurements conducted on our recently developed tandem-trapped ion mobility spectrometry (TIMS/TIMS-MS) instrument. We elucidate detailed structure for a number of protein systems, including the small protein ubiquitin (8.6 kDa), ribonuclease A and its glycosylated variants ribonuclease B, and the protein complex avidin. Avidin is a homotetrameric glycoprotein complex with 128 amino acids in each subunit. At least eight different glycoform variants have been reported for avidin monomers. Our contribution discusses how we characterize presence of glycoforms on our tandem-trapped ion mobility spectrometry / mass spectrometry instrument and then use our computational methods to relate presence of glycoforms regulates the avidin tertiary and quaternary structures. Overall, our analysis reveals that even small protein ions detected from native conditions by soft ion mobility measurements largely retain their hydrophobic core present in their native structure as well as their native inter-residue contacts and secondary-structure elements.

Tandem-trapped ion mobility/mass spectrometry measurements relates proteoform identity to their tertiary and quaternary structures

2019 Fall National Meeting

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