Synthetic oligonucleotides and their analogs have shown promising potential therapeutic agents in the treatment of viral infections and certain cancers. As drugs, the full characterization of oligonucleotides requires complete verification. Chromatographic or electrophoretic techniques can be used in analysis of concentration and purity of synthetic oligonucleotides, but the analytic methods have been limited in analysis of base composition, sequence, identity and modification of oligonucleotides. Ability of mass spectrometry to discriminate mass make MS effective, sensitive, rapid and accurate to determine these characterizations of oligonucleotides. application of mass spectrometry in quality control of synthetic oligonucleotides was introduced.