Interpretation of Oligonucleotide Mass Spectra for Determination of Sequence Using Electrospray Ionization and Tandem Mass Spectrometry

• Published in: Analytical chemistry (Washington) 1996-07, Vol.68 (13), p.1989-1999
• Main Authors: Ni, Jinsong, Pomerantz, Steven C, Rozenski, Jef, Zhang, Yizhou, McCloskey, James A
• Format: Article
• Language: English
• Subjects: Algorithms; Analytical, structural and metabolic biochemistry; Base Sequence; Biological and medical sciences; Biotechnology; Chemistry; Fundamental and applied biological sciences. Psychology; General aspects, investigation methods; Genetic engineering; Genetic technics; Ions; Mass Spectrometry; Methods. Procedures. Technologies; Molecular Sequence Data; Nucleic acids; Oligonucleotides - analysis; Scientific imaging; Sequence Analysis, DNA - methods; Sequence Analysis, RNA - methods; Synthetic digonucleotides and genes. Sequencing
• ISSN: 0003-2700; 1520-6882
• DOI: 10.1021/ac960270t

Procedures are described for interpretation of mass spectra from collision-induced dissociation of polycharged oligonucleotides produced by electrospray ionization. The method is intended for rapid sequencing of oligonucleotides of completely unknown structure at approximately the 15-mer level and below, from DNA or RNA. Identification of sequence-relevant ions that are produced from extensive fragmentation in the quadrupole collision cell are based primarily on (1) recognition of 3‘- and 5‘-terminal residues as initial steps in mass ladder propagation, (2) alignment of overlapping nucleotide chains that have been constructed independently from each terminus, and (3) use of experimentally measured molecular mass in rejection of incorrect sequence candidates. Algorithms for sequence derivation are embodied in a computer program that requires