TY  - JOUR
A1  - Villatoro, José Andrés
A1  - Weber, M.
A1  - Zühlke, Martin
A1  - Lehmann, A.
A1  - Zenichowski, Karl
A1  - Riebe, Daniel
A1  - Beitz, Toralf
A1  - Löhmannsröben, Hans-Gerd
A1  - Kreuzer, O.
T1  - Structural characterization of synthetic peptides using electrospray ion mobility spectrometry and molecular dynamics simulations
JF  - International Journal of Mass Spectrometry
N2  - Electrospray ionization-ion mobility spectrometry was employed for the determination of collision cross sections (CCS) of 25 synthetically produced peptides in the mass range between 540-3310 Da. The experimental measurement of the CCS is complemented by their calculation applying two different methods. One prediction method is the intrinsic size parameter (ISP) method developed by the Clemmer group. The second new method is based on the evaluation of molecular dynamics (MD) simulation trajectories as a whole, resulting in a single, averaged collision cross-section value for a given peptide in the gas phase. A high temperature MD simulation is run in order to scan through the whole conformational space. The lower temperature conformational distribution is obtained through thermodynamic reweighting. In the first part, various correlations, e.g. CCS vs. mass and inverse mobility vs. m/z correlations, are presented. Differences in CCS between peptides are also discussed in terms of their respective mass and m/z differences, as well as their respective structures. In the second part, measured and calculated CCS are compared. The agreement between the prediction results and the experimental values is in the same range for both calculation methods. While the calculation effort of the ISP method is much lower, the MD method comprises several tools providing deeper insights into the conformations of peptides. Advantages and limitations of both methods are discussed. Based on the separation of two pairs of linear and cyclic peptides of virtually the same mass, the influence of the structure on the cross sections is discussed. The shift in cross section differences and peak shape after transition from the linear to the cyclic peptide can be well understood by applying different MD tools, e.g. the root-mean-square deviation (RMSD) and the root mean square fluctuation (RMSF). (C) 2018 Elsevier B.V. All rights reserved.
KW  - Ion mobility spectrometry
KW  - Electrospray ionization
KW  - Peptides
KW  - Collision cross-section
KW  - Molecular dynamics
Y1  - 2019
U6  - https://doi.org/10.1016/j.ijms.2018.10.036
SN  - 1387-3806
SN  - 1873-2798
VL  - 436
SP  - 108
EP  - 117
PB  - Elsevier
CY  - Amsterdam
ER  -