Matrix-assisted laser desorption/ionization mass spectrometry for the structural characterization of modified oligonucleotides

Abstract

Matrix‐assisted laser desorption ionization (MALDI) Fourier transform ion cyclotron resonance mass spectrometry (FTMS) and MALDI time‐of‐flight mass spectrometry (TOFMS) are being used to characterize conditions for the efficient desorption and ionization of normal and modified nucleic acid components. Basic and acidic matrix materials have been evaluated on the components. Basic and acidic matrix materials have been evaluated on the FTMS and TOFMS. Using MALDI‐FTMS at 355 nm, less fragmentation has been observed using 2,5‐dihydroxybenzoic acid, while more extensive fragmentation is observed for basic matrices, such as 1,5‐diaminonaphthalene and 9‐aminophenanthrene. Elevation of the cell pressure by the addition of Ar or CO2 provides collisional cooling of desorbed ions, resulting in an enhancement of [M–H]− and structurally significant high‐mass fragment ions. Using MALDI‐TOFMS at 337 nm, fragmentation is significantly reduced relative to that observed on the FTMS, perhaps as a consequence of the longer times required for FTMS detection. On the FTMS and TOFMS, cluster ions have been observed in the negative ion mode when metal ions are present in the 2,5‐dihydroxybenzoic acid matrix. Metal ion additions and clusters with matrix salts have also been observed for dinucleotides. Applications of MALDI‐FTMS and MALDI‐TOF to the detection of hydroxylated PAH nucleoside adducts are presented.