Ion mobility-mass spectrometry (IM-MS) has been used to study the gas-phase structures of three proteins: the DNA-binding core domain of p53 (amino acid residues 94-312) and two fragments of complement control protein factor H (regions 10-15 and 19-20) which are involved in important cellular processes. We report collision cross-sections as a function of charge state for these systems, following electrospray ionisation from 'native' conditions. The DNA-binding core domain of p53 contains a zinc ion that is postulated to have an important role in retaining functionality. We have chelated the zinc from the protein using phenanthroline and observed the conformational change in collision cross-section. Factor H region 10-15 has been interrogated and cross-sections have been elucidated for this recombinant protein that contains a number of covalently bound N-acetylglucosamine sugar molecules. Factor H region 19-20 is proposed to be an important polyanion-binding site for the intact factor H molecule (regions 1-20,1213 amino acid residues in total) and characterising its structure by IM-MS has provided further information to the overall structure of the Factor H protein. This work employs two different IM-MS instruments: the commercially available Waters Synapt HDMS instrument, and our Mobility Q-TOF ("MoQTOF") developed in house. Collision cross-sections obtained from identical molecular species differ to some extent between the two instruments. We observe some good agreement and some variation, with a general trend being that systems examined on the MoQTOF possess and present more compact collision cross-sections than observed with the same species on the Synapt. We attribute these differences principally to slight variations in solution conditions, effecting solution conformations and also to the differences in the source conditions and the ion transmission to the mobility devices affecting gas-phase conformations. (C) 2010 Elsevier B.V. All rights reserved.