Direct mass spectrometric sequencing of low‐picomole amounts of oligodeoxynucleotides with up to 21 bases by matrix‐assisted laser desorption/ionization mass spectrometry

UV and IR matrix-assisted laser desorption/ionization mass spectrometry (UV- and IR-MALDI) have demonstrated their potential for the accurate and sensitive mass determination of oligonucleotides. Metastable molecule ion fragmentation was found to be the main limitation in both desorption schemes for the analysis of larger nucleic acid sequences. Fragment ions from additional prompt decays, observed only in IR-MALDI, offer structural data, which allow sequence information to be derived for low-picomole amounts of oligodeoxynucleotides with up to 21 bases from a single mass spectrum. Two examples demonstrating the feasibility of this new sequencing technique are given. A model is introduced and discussed, which proposes a reaction scheme for the observed fragment ion patterns of nucleic acids and differentiates prompt and metastable fragmentation mechanisms. The role of fragmentation in direct mass spectrometric sequencing schemes and as a limitation for the accessible mass range in nucleic acid MALDI mass spectrometry is discussed.