Enhanced in-source fragmentation in MALDI-TOF-MS of oligonucleotides using 1,5-diaminonapthalene

Nathan A. Hagan, Christine A. Smith, Miquel D. Antoine, Jeffrey S. Lin, Andrew B. Feldman, Plamen A. Demirev

Research output: Contribution to journalArticlepeer-review

10 Scopus citations


The capability to rapidly and confidently determine or confirm the sequences of short oligonucleotides, including native and chemically-modified DNA and RNA, is important for a number of fields. While matrix-assisted laser desorption/ionization (MALDI) time-of-flight (TOF) mass spectrometry (MS) has been used previously to sequence short oligonucleotides, the typically low fragmentation efficiency of in-source or post-source decay processes necessitates the accumulation of a large number of spectra, thus limiting the throughput of these methods. Here we introduce a novel matrix, 1,5-diaminonapthalene (DAN), for facile in-source decay (ISD) of DNA and RNA molecular anions, which allows for rapid sequence confirmation. d-, w-, and yseries ions are prominent in the spectra, complementary to the (a-B)- and w- ions that are typically produced by MALDI post-source decay (PSD). Results are shown for several model DNA and RNA oligonucleotides, including combinations of DAN-induced fragmentation with true tandem TOF MS (MS/MS) for pseudo-MS 3 and "activated-ion PSD."

Original languageEnglish (US)
Pages (from-to)773-777
Number of pages5
JournalJournal of the American Society for Mass Spectrometry
Issue number4
StatePublished - Apr 2012
Externally publishedYes


  • 1,5-Diaminonapthalene
  • DNA
  • In-Source decay
  • Matrix-assisted laser desorption/ionization
  • RNA

ASJC Scopus subject areas

  • Structural Biology
  • Spectroscopy


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