Comparison of gaseous ubiquitin ion structures obtained from a solid and solution matrix using ion mobility spectrometry/mass spectrometry

Rationale Examining surface protein conformations, and especially achieving this with spatial resolution, is an important goal. The recently discovered ionization processes offer spatial‐resolution measurements similar to matrix‐assisted laser desorption/ionization (MALDI) and produce charge states similar to electrospray ionization (ESI) extending higher‐mass protein applications directly from surfaces on high‐performance mass spectrometers. Studying a well‐interrogated protein by ion mobility spectrometry‐mass spectrometry (IMS‐MS) to access effects on structures using a solid vs. solvent matrix may provide insights. Methods Ubiquitin was studied by IMS‐MS using new ionization processes with commercial and homebuilt ion sources and instruments (Waters SYNAPT G2(S)) and homebuilt 2 m drift‐tube instrument; MS™ sources). Mass‐to‐charge and drift‐time (td)‐measurements are compared for ubiquitin ions obtained by inlet and vacuum ionization using laserspray ionization (LSI), matrix‐ (MAI) and solvent‐assisted ionization (SAI), respectively, and compared with those from ESI under conditions that are most comparable. Results Using the same solution conditions with SYNAPT G2(S) instruments, td‐distributions of various ubiquitin charge states from MAI, LSI, and SAI are similar to those from ESI using a variety of solvents, matrices, extraction voltages, a laser, and temperature only, showing subtle differences in more compact features within the elongated distribution of structures. However, on a homebuilt drift‐tube instrument, within the elongated distribution of structures, both similar and different td‐distributions are observed for ubiquitin ions obtained by MAI and ESI. MAI‐generated ions are frequently narrower in their td‐distributions. Conclusions Direct comparisons between ESI and the new ionization methods operational directly from surfaces suggest that the protein in its solution structure prior to exposure to the ionization event is either captured (frozen out) at the time of crystallization, or that the protein in the solid matrix is associated with sufficient solvent to maintain the solution structure, or, alternatively, that the observed structures are those related to what occurs in the gas phase with ESI‐ or MAI‐generated ions and not with the solution structures.