Accurate molecular weight measurements of nucleoside phosphoramidites: a suitable matrix of mass spectrometry

Nucleoside phosphoramidites (PAs) are the most widely used building blocks in contemporary solid-phase synthesis of oligonucleotides. The accurate molecular weight (MW) measurements of such molecules, which contain acid-labile moieties, may be easily determined by mass spectrometry using a matrix system, triethanolamine (TEOA)–NaCl, on liquid secondary ion mass spectrometry (LSIMS) equipped with a double-focusing mass spectrometer. The present method measures rapidly and easily the accurate MWs of various PAs as adduct ions [M+Na]+ with average mass error smaller than 0.4 ppm, allowing the formulas of various PAs in place of elemental analysis. Further, it was found that intensities of molecular-related ions could be enhanced to the highest degree by adjustment of the mole ratio of PA and NaCl fixing the amount of TEOA on LSIMS, making the present method powerful tool for the MS identification of PAs.