Determining if a specific proline is cis or trans in the protein?
Sarkar et al.(2007) Proline cis-trans Isomerization Controls Autoinhibition of a Signaling Protein. Molecular Cell 25, 413–426 (DOI 10.1016/j.molcel.2007.01.004), available here. 


The authors report on the interactions between two SH3 domains of the Crk adaptor protein. Basically they find that the linker which tethers these two domains contains a proline which interconverts between the cis and trans conformations, and that this interconversion determines the interaction between the two domains. They follow isomerisation by using NMR.

Cis-trans peptidyl-prolyl isomerization is a subtle change, and I don't think that you will find a way of following it in a specific protein that is simpler than this, unfortunately.