For almost three decades, gene therapy has been gaining interest to efficiently treat some severe diseases. In such context, the discovery of an efficient non-viral gene carrier to deliver genetic material into targeted cell nuclei is of prime importance. Numerous synthetic vectors that have been designed exhibit high transfection efficiency but also suffer from extensive cytotoxicity, thus justifying efforts to synthesize more bio-compatible ones, for example, with carbohydrate scaffolds. In this sense, cyclodextrins (CDs) are well known to present low to very low cytotoxicity in humans and have potential, after polycationization, to serve as suitable compaction/transfection agents for RNA/DNA. However, such polycationic CDs must be accurately characterized to establish a straightforward structure–biological activity relationship which is guided by the nitrogen/phosphorus ratio (N/P). In the study herein, we demonstrated that electrospray-(tandem) mass spectrometry (ESI-(MS)MS) combining Collision Induced Dissociation (CID) and Higher Collision induced Dissociation (HCD) is a useful tool for such synthetic agent characterization. The suitability of CID/HCD pairwise combination was investigated for the structural deciphering of five representative members of a polycationic cyclodextrin library. Our approach allows for easy access to content, type and localisation of amino groups thereby offering a useful tool to correlate the synthetic delivery agent with effective compaction of oligo-/polynucleotides.