Electrospray droplet exposure to gaseous acids for reduction of metal counter-ions in nucleic acid ions

Abstract

Electrospray ionization (ESI) of oligonucleotides in either polarity mode often yields a distribution of ions at each charge state that vary in the number and identities of metal counter-ions present, thereby complicating the appearance of the mass spectrum. A variety of approaches designed to treat or modify the solution subjected to ESI have been introduced to deal with this issue. A new procedure has been developed in which chemical vapors are introduced into a region prior to the atmosphere/vacuum interface of a QqTOF instrument along with the usual counter-current nitrogen gas intended to facilitate droplet desolvation. Acidic vapors can be introduced to shift the charge state distribution of samples subjected to either positive or negative nanoelectrospray ionization as well as to reduce the number of metal counter-ions observed in DNA, siRNA and LNA ions. To remove the metal counter-ions and improve the signal levels when ionizing in the negative nanoelectrospray mode, vapors of weak acids such as acetic acid and formic acid can be mixed with the curtain gas and introduced in front of the instrument interface. For positive nanoelectrospray generated ions, the introduction of strong acids such as hydrochloric acid and trifluoroacetic acid helps to reduce the metal counter-ion incorporation and results in an increase in signal levels. The vapor addition approach is not equivalent to adding acid directly in the solution as it preserves non-covalent interactions, as seen with the preservation of the siRNA duplex during acid vapor introduction into the interface.