Biopolymer analysis by electrospray ionization and tandem mass spectrometry

Electrospray ionization was used in conjunction with Fourier-transform ion cyclotron resonance (FTICR) mass spectrometry and quadrupole ion trap (QIT) mass spectrometry to study protein and oligonucleotide ions in vacuo. The results help to identify effective strategies for mass spectral analysis of these macromolecules and provide new insight on their gas-phase behavior. Tandem mass spectrometry experiments were conducted to evaluate different ion activation methods for biopolymer sequencing. Multipole storage-assisted dissociation (MSAD) and sustained off-resonance irradiation collision-activated dissociation (SORI- CAD) were compared for protein analysis in FTICR instrumentation, and infrared multiphoton dissociation (IRMPD) and collisonal activated dissociation (CAD) were compared for oligonucleotide analysis in QIT instrumentation. In both studies, the differences in the observed fragmentation patterns were noted and the underlying reasons for these differences were identified. The relative utility of MSAD vs. SORI-CAD and IRMPD vs. CAD were assessed in terms of their ability to produce diagnostic information that could be used to identify the protein or oligonucleotide under study. Tandem mass spectrometry was also employed to study the dissociation patterns of both DNA/metal and DNA/drug complexes. The preferred fragmentation pathways exhibited by these species were observed to vary with the initial charge state of the precursor. The effect of the oligonucleotide sequence, the identity of the metal ion, and the identity of the drug on these pathways was established and (where possible) interpreted in terms of the specific non-covalent bonding patterns present in the parent complexes. Finally, electrospray ionization was evaluated as a tool for screening molecular recognition in nucleic acid aptamer/small molecule interactions. Gas-phase data for binding stoichiometry and relative binding affinity were compared with the known solution behavior for a series of well-characterized case studies. Any observed discrepancies were rationalized in terms of ligand structure and/or the nature of the intermolecular ligand/aptamer interactions.