Enhanced in-source fragmentation in MALDI-TOF-MS of oligonucleotides using 1,5-diaminonapthalene.
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 y-series 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."
Johns Hopkins University Applied Physics Laboratory, Laurel, MD 20723, USA. nathan.hagan@jhuapl.edu
Nathan A
NA
Hagan
Christine A
CA
Smith
Miquel D
MD
Antoine
Jeffrey S
JS
Lin
Andrew B
AB
Feldman
Plamen A
PA
Demirev
D015081:2-Naphthylamine / Q000031:analogs & derivatives* / Q000737:chemistry; D000838:Anions / Q000737:chemistry; D004247:DNA / Q000737:chemistry; D008956:Models, Chemical; D009841:Oligonucleotides / Q000737:chemistry*; D012313:RNA / Q000737:chemistry; D019032:Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization / Q000379:methods*
D000838:Anions; D009841:Oligonucleotides; C510889:1,5-diaminonaphthalene; D012313:RNA; D004247:DNA; D015081:2-Naphthylamine