Enhanced gas-phase hydrogen-deuterium exchange of oligonucleotide and protein ions stored in an external multipole ion reservoir

Rapid gas-phase hydrogen-deuterium (H-D) exchange from D(2)O and ND(3) into oligonucleotide and protein ions was achieved during storage in a hexapole ion reservoir. Deuterated gas is introduced through a capillary line that discharges directly into the low-pressure region of the reservoir. Following exchange, the degree of H-D exchange is determined using Fourier transform ion cyclotron resonance mass spectrometry. Gas-phase H-D exchange experiments can be conducted more than 100 times faster than observed using conventional in-cell exchange protocols that require lower gas pressures and additional pump-down periods. The short experimental times facilitate the quantitation of the number of labile hydrogens for less reactive proteins and structured oligonucleotides. For ubiquitin, we observe approximately 65 H-D exchanges after 20 s. Exchange rates of > 250 hydrogens s(-1) are observed for oligonucleotide ions when D(2)O or ND(3) is admitted directly into the external ion reservoir owing to the high local pressure in the hexapole. Partially deuterated oligonucleotide ions have been fragmented in the reservoir using infrared multiphoton dissociation (IRMPD). The resulting fragment ions show that exchange predominates at charged sites on the 5'- and 3'-ends of the oligonucleotide, whereas exchange is slower in the core. This hardware configuration is independent of the mass detector and should be compatible with other mass spectrometric platforms including quadrupole ion trap and time-of-flight mass spectrometers.