SOS: a simple interactive program for ab initio oligonucleotide sequencing by mass spectrometry

Journal of the American Society for Mass Spectrometry
J Rozenski, J A McCloskey

Abstract

Mass spectra of oligonucleotides derived from collision-induced dissociation following electrospray ionization provide an effective means of sequence determination, at the 20-mer level and below. An interactive, stand-alone computer program, Simple Oligonucleotide Sequencer (SOS) has been developed for rapid oligonucleotide sequencing from mass spectra, under user control on a residue by residue basis. Modifications can be defined in any combination for the base, sugar or backbone. Sequence ladders can be independently constructed in both the 5' --> 3' directions and 3' --> 5' directions, and graphically compared for homology and overlap. A particular advantage of this method is the ability to easily erase and rebuild alternate subsequences. The program can be used for ab initio sequencing of modified or unmodified oligonucleotides, for rapid verification of sequence, and in studies of fragmentation processes of model oligonucleotide derivatives.

References

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Citations

Dec 25, 2012·Journal of the American Society for Mass Spectrometry·Adrien NyakasStefan Schürch
Jun 7, 2013·Journal of the American Society for Mass Spectrometry·Jiong YangFanyu Meng
Dec 31, 2003·Journal of the American Society for Mass Spectrometry·Herbert OberacherChristian G Huber
Mar 30, 2004·Journal of the American Society for Mass Spectrometry·Herbert OberacherChristian G Huber
Aug 11, 2006·Journal of the American Society for Mass Spectrometry·Arthur Van Aerschot, Jef Rozenski
Feb 28, 2013·Chemical Reviews·Natalia TretyakovaSrikanth Kotapati
Aug 23, 2012·The Journal of Biological Chemistry·Linlin ZhaoF Peter Guengerich
Jun 14, 2006·Briefings in Functional Genomics & Proteomics·Zhaojing Meng, Patrick A Limbach
May 8, 2014·Journal of the American Society for Mass Spectrometry·Adrien NyakasStefan Schürch
Feb 4, 2009·Biopolymers·Herbert Oberacher, Florian Pitterl
Jan 10, 2012·Journal of Mass Spectrometry : JMS·Silvan R StuckiStefan Schürch
Aug 27, 2010·Rapid Communications in Mass Spectrometry : RCM·Vera B IvlevaMartin Gilar
Sep 11, 2013·Rapid Communications in Mass Spectrometry : RCM·Henry C FisherAlison E Ashcroft
Apr 2, 2016·Methods : a Companion to Methods in Enzymology·Robert RossPatrick A Limbach
Feb 18, 2006·Trends in Biochemical Sciences·Benjamin Thomas, Alexandre V Akoulitchev
Feb 18, 2011·Mass Spectrometry Reviews·Hiroshi NakayamaToshiaki Isobe
Jun 5, 2015·Journal of the American Society for Mass Spectrometry·Brett HarperTouradj Solouki
Sep 29, 2011·Journal of Chromatography. B, Analytical Technologies in the Biomedical and Life Sciences·A Cary McGinnisMichael G Bartlett
Jul 22, 2014·Bioanalysis·Babak Basiri, Michael G Bartlett
Sep 30, 2016·Nucleic Acids Research·Juthamas JaroensukMayuree Fuangthong
Nov 12, 2016·Nature Communications·Yok Hian ChionhPeter C Dedon
Jul 19, 2002·Journal of Mass Spectrometry : JMS
Jun 10, 2010·European Journal of Mass Spectrometry·Herbert Oberacher
Jul 28, 2005·European Journal of Mass Spectrometry·Zhaojing Meng, Patrick A Limbach
Oct 20, 2006·The Journal of Biological Chemistry·Jeong-Yun ChoiF Peter Guengerich

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