Will proteins eluted in the Qproteome Plasma Membrane Protein protocol be modified, e.g. with the ligand?

No, proteins eluted when using the Qproteome Plasma Membrane Protein Kit will not be modified. Plasma membrane vesicles are eluted off the ligand under native conditions, and the ligand remains bound to the beads. The final product is endogenous, active plasma membrane protein packed in small plasma membrane vesicles, and is suitable for functional studies downstream.