Characterization of supramolecular peptide-polymer bioconjugates using multistage tandem mass spectrometry

Electrospray ionization multistage tandem mass spectrometry (ESI-MSⁿ) was employed to examine the non-covalent complexes between poly(styrene sulfonate) (PSS) and poly-L-lysine (PLL). During single-stage ion activation, the PLL peptide chain mainly underwent backbone cleavages without disruption of the non-covalent interaction which could only be broken via sequential application of electron transfer dissociation (ETD) and collisionally activated dissociation (CAD), indicating strong binding interactions between the two polyelectrolyte chains. Such binding properties make PSS a potential “non-covalent (supramolecular) label” for determining the surface accessibility of basic residues on a peptide or protein. To probe this premise, non-covalent complexes of substance P and PSS were characterized by ESI-MSⁿ using different ion activation methods. Both MS² and MS³ experiments on the substance P + PSS complex resulted in the formation of b_n (on CAD) or c_n (on ETD) fragments attached non-covalently to the intact PSS chain. All peptide fragments containing the intact PSS chain included Arg1, Lys3, and Gln5, pointing out that these residues, which are located near the N-terminus, are most likely involved in the non-covalent interaction with PSS. In contrast, Gln6 was excluded from this fragment series, attesting a much weaker interaction with PSS due to lesser accessibility. The strong tendency of PSS to bind peptides non-covalently at sites that can be elucidated by MSⁿ demonstrates a proof-of-concept for the capacity of this approach to unveil higher order structure in proteins.