First-Principles Collision Cross Section Measurements of Large Proteins and Protein Complexes.

Rotationally averaged collision cross section (CCS) values for a series of proteins and protein complexes ranging in size from 8.6 to 810 kDa are reported. The CCSs were obtained using a native electrospray ionization drift tube ion mobility-Orbitrap mass spectrometer specifically designed to enhance sensitivity while having high-resolution ion mobility and mass capabilities. Periodic focusing (PF)-DT-IM provides first-principles determination of CCS of large biomolecules that can then be used as CCS calibrants. The experimental, first-principles CCS values are compared to previously reported experimentally determined and computationally calculated CCS using PSA, IMPACT, and Collidoscope. Experimental CCS values are generally in agreement with previously reported CCS, with values falling within ~5.5%. In addition, an ion mobility resolution (CCS centroid divided by CCS FWHM) of ~60 is obtained for pyruvate kinase (MW ~233 kDa); however, ion mobility resolution for bovine serum albumin (MW ~68 kDa) is less than ~20, which arises from sample impurities and underscores the importance of sample quality. The high resolution afforded by the ion mobility-Orbitrap mass analyzer provides new opportunities to understand the intricate details of protein complexes such as the impact of post-translational modifications (PTMs), stoichiometry, and conformational changes induced by ligand binding.