The use of a stable internal mass standard for accurate mass measurements of oligonucleotide fragment ions using electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry with infrared multiphoton dissociation

In this work we demonstrate the use of peptide as a stable internal mass standard to obtain accurate mass measurements of infrared multiphoton dissociation (IRMPD) generated phosphorothioate oligonucleotide fragment ions. Because oligonucleotides are more readily dissociated in the gas phase by IRMPD than are proteins or peptides, the duration and power of the IRMPD event can be set above the oligonucleotide dissociation threshold without inducing fragmentation of the internal peptide standard. This concept is illustrated with electrospray ionization fourier transform ion cyclotron resonance IRMPD of a 20-mer phosphorothioate oligonucleotide in the presence of a small amount of insulin a-chain. Using several isotope peaks from multiple charge states of the a-chain as an internal mass standard provides low-ppm mass measurement errors for the IRMPD generated phosphorothioate oligonucleotide fragment ions. In addition to simplifying the assignment of fragment ions generated from IRMPD of oligonucleotides, this method should be directly applicable to the characterization of DNA and RNA adducts and other base modifications, and may facilitate elemental composition determinations of adducts and base modifications from the resulting mass measurements.