UNIT 10.11 Mass Determination of Phosphoramidites

  1. Shinya Harusawa1,
  2. Mihoyo Fujitake1,
  3. Takushi Kurihara1,
  4. Zheng-yun Zhao2,
  5. David M.J. Lilley2

Published Online: 1 OCT 2006

DOI: 10.1002/0471142700.nc1011s26

Current Protocols in Nucleic Acid Chemistry

Current Protocols in Nucleic Acid Chemistry

How to Cite

Harusawa, S., Fujitake, M., Kurihara, T., Zhao, Z.-y. and Lilley, D. M. 2006. Mass Determination of Phosphoramidites. Current Protocols in Nucleic Acid Chemistry. 26:10.11:10.11.1–10.11.16.

Author Information

  1. 1

    Osaka University of Pharmaceutical Sciences, Osaka, Japan

  2. 2

    University of Dundee, Dundee, Scotland

Publication History

  1. Published Online: 1 OCT 2006
  2. Published Print: SEP 2006


Nucleoside phosphoramidites are the most widely used building blocks in contemporary solid-phase synthesis of oligonucleotides. The accurate molecular weight measurements of such molecules, which are acid-labile compounds, may be easily determined by mass spectrometry using a matrix system, triethanolamine/NaCl, on a liquid secondary ion mass spectrometer (LSIMS) or fast-atom bombardment (FAB) MS equipped with a double-focusing mass spectrometer. The present method rapidly and easily measures the accurate molecular weights of various phosphoramidites as adduct ions [M+Na]+ with an average mass error smaller than 0.4 ppm, allowing determination of the formulas of the phosphoramidites 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 molar ratio of phosphoramidite and NaCl, fixing the amount of triethanolamine on LSIMS, making the present method a powerful tool for identification of phosphoramidites by mass spectrometry.


  • nucleoside;
  • phosphoramidite;
  • molecular weight;
  • mass spectrometry;
  • matrix