A new approach is described for the elucidation of gas-phase peptide ion structures
combining ion mobility spectrometry (IMS) data and molecular dynamics (MD)-cluster
analysis (CA) prediction. The new approach is based on the determination of the gas-phase
ion structure identity vectors (e.g., structure and population vectors) that generate
the total conformational space of the gas-phase ion as a function of the IMS experimental
conditions (e.g., field strength, pressure, bath gas temperature, and IM cell geometry).
Two methods to efficiently sample the gas-phase conformational space of molecular
ions as a function of the effective ion temperature characteristic of the IMS experiments
are described: (i) a simulated annealing MD-CA-constant temperature MD-CA, and (ii)
a generalized non-Boltzmann sampling MD-free energy analysis-CA. The new theoretical
method has been successfully applied to two model peptide ions (Bradykinin fragments
1-5 and 1-8, RPPGF and RPPGFSPF, respectively) for which multiple conformations sensitive
to the effective ion temperature have been suggested in previous studies.