Resolution and structural transitions of elongated states of ubiquitin

Electrospray ionization, combined with two-dimensional ion mobility spectrometry and mass spectrometry, is used to produce, select, and activate distributions of elongated ions, [M ϩ 11H] 11ϩ to [M ϩ 13H] 13ϩ , of ubiquitin. The analysis makes it possible to examine state-to-state transitions for structural types, and transition diagrams associated with the efficiencies of structural changes are presented. The ϩ11 and ϩ12 charge states can form four resolvable states while only one state is formed for [M ϩ 13H] 13ϩ . Some conformations, which appear to belong to the same family based on mobility analysis of different charge states, undergo similar transitions, others do not. Activation of ions that exist in low-abundance conformations, having mobilities that fall in between sharp peaks associated with higher abundances species, shows that the low-abundance forms undergo efficient (ϳ90 to 100%) conversion into states associated with well-defined peaks. This efficiency is significantly higher than the ϳ10 to 60% efficiency of transitions of structures associated with well-defined peaks. The formation of sharp features from a range of low-intensity species with different cross sections indicates that large regions of conformation space must be unfavorable or inaccessible in the gas phase. These results are compared with several previous IMS measurements of this system as well as information about gas-phase structure provided by other techniques. Studies of solvent-free proteins and peptides are important because of both fundamental and practical considerations. In the absence of solvation shells (or with minimal solvent), it is possible to extract kinetic and thermodynamic benchmarks about the formation of specific types of folds and tease out the influence of solvent-molecule and intramolecular factors in establishing conformation [2] A number of groups have worked to combine ion mobility spectrometry (IMS) and MS with the aim of using differences in ion mobility to separate components of a mixture that would not be resolved by MS alone [21, 22]. The mobility of a macromolecular ion through a buffer gas depends on its charge and shape (average collision cross section with the buffer gas, ⍀). Recently, we have ex- tended a hybrid IMS/MS instrument to include additional IMS dimensions leading to IMS-IMS/MS and IMS-IMS-IMS/MS instrument designs As one develops new IMS techniques (as well as other methods) it is important to revisit model systems, where some fundamental understanding of the nature of the system exists. In the present paper, we focus on the ϩ11 to ϩ13 charge states of ubiquitin ions produced by standard ESI conditions. Ubiquitin is a small, 76 amino acid protein that, under most ESI source conditions, favors the ϩ5 to ϩ13 charge states [27

Mapping the proteome of Drosophila melanogaster: analysis of embryos and adult heads by LC-IMS-MS methods. JProteomeRes 2005;4

Multidimensional separations combined with mass spectrometry are used to study the proteins that are present in two states of Drosophila melanogaster: the whole embryo and the adult head. The approach includes the incorporation of a gas-phase separation dimension in which ions are dispersed according to differences in their mobilities and is described as a means of providing a detailed analytical map of the proteins that are present. Overall, we find evidence for 1133 unique proteins. In total, 780 are identified in the head, and 660 are identified in the embryo. Only 307 proteins are in common to both developmental stages, indicating that there are significant differences in these proteomes. A comparison of the proteome to a database of mRNAs that are found from analysis by cDNA approaches (i.e., transcriptome) also shows little overlap. All of this information is discussed in terms of the relationship between the predicted genome, and measured transcriptomes and proteomes. Additionally, the merits and weaknesses of current technologies are assessed in some detail