We employ Cold Ion Spectroscopy (CIS) in conjunction with high-Field Asymmetric Waveform Ion Mobility Spectrometry (FAIMS) to study the peptide bradykinin in its doubly protonated charge state ([bk+2H]2+). Using FAIMS we partially separate the electrosprayed [bk+2H]2+ ions into two conformational families and selectively introduce one of them at a time into a cold ion trap mass spectrometer, where we probe them by UV photofragment spectroscopy. Although the two conformational families have distinct electronic spectra, some cross-conformer contamination can be observed under certain conditions. We demonstrate that this contamination comes from isomerization of ions energized during and/or after their separation and not from incomplete separation of the initially electrosprayed conformations in the FAIMS stage. By varying the injection voltage of the ions into our mass spectrometer we can intentionally induce isomerization to produce what seems to be a gas phase equilibrium distribution of conformers. This distribution is different from the one produced initially by electrospray, indicating that some of the conformers are kinetically trapped and may be related to conformers that are more favored in solution.