Electrospray mass spectrometry of phosphoramidites, a group of acid-labile compounds

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In contemporary solid-phase synthesis of oligonucleotides, phosphoramidites containing O-β-cyanoethyl and N,N-diisopropyl groups are the most widespread monomer units. The N,N-diisopropyl phosphoramidite group can be activated by mild acidic treatment and then it easily reacts with nucleophiles (alcohols, water, etc.) to furnish the required phosphodiester linkage efficiently and cleanly. Owing to these properties, these compounds cannot be investigated using classical electrospray ionization. Their mass spectometric analysis is further hampered by the fact that they are often transiently protected with acid-sensitive groups (4,4'-dimethoxytrityl, 4-monomethoxytrityl or trityl), which give intense signals in the spectra. Nanoelectrospray measurements from non-aqueous solvents (e.g. acetonitrile, methanol, tetrahydrofuran) were carried out in order to eliminate the nucleophilic water. Different types of alkali metal salts were used to form adduct ions. Among these salts, lithium chloride was found to be the most suitable for the analysis of amidites. Fairly abundant [M + Li]+ and [M + Cl]- ions are formed in the positive and negative ion mode, respectively. These ions represent the base peaks in most cases whereas the intensities of the peaks corresponding to the protecting group are reduced by ~20%. This method is a powerful tool for the mass spectrometric identification of phosphoramidites.

Original languageEnglish
Pages (from-to)1317-1321
Number of pages5
JournalJournal of Mass Spectrometry
Issue number12
Publication statusPublished - Dec 1 1999


  • Acid-labile
  • Nanoelectrospray mass spectrometry
  • Non-aqueous
  • Phosphoramidites

ASJC Scopus subject areas

  • Spectroscopy

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