Abstract

European Journal of Mass Spectrometry
Volume 12 Issue 3, Pages 205–211 (2006)
doi: 10.1255/ejms.800

Analysis of single nucleotide polymorphism sites in exon 4 of the p53 gene using high-performance liquid chromatography electrospray ionization mass spectrometry tandem mass spectrometry

Renfang Song,^a,b Wenbing Zhang,^a Huayong Chen,^a,b Huimin Ma,^a,b Yulian Dong,^a Guoying Sheng,^a Zhen Zhou^a and Jiamo Fu^a,*
aState Key Laboratory of Organic Geochemistry, Guangzhou Research Center of Mass Spectrometry, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China. E-mail: fujm@gig.ac.cn
^bGraduate School of the Chinese Academy of Sciences, Beijing, China

Three groups of four oligonucleotides with special single nucleotide polymorphisms (SNP) sites in exon 4 of the p53 gene were analyzed with ion-pair reversed-phase high-performance liquid chromatography electrospray ionization mass spectrometry tandem mass spectrometry. The retention order of four oligonucleotides with SNPs was C < G < A < T, regardless of whether the polymorphisms were at the 3′ end, the 5′ end, or the middle of the oligonucleotides. The charge state of the molecular ion affects the MS/MS spectra of the oligonucleotides. SNPs at the 3′ end can be easily identified from the fragmentation pattern of the 2- charge state, but not from the 3- charge state, especially from the w1 fragment. The single base may be taken as the symbol of the 5′ end SNP site derived from [M–3H]^2–, but not from the [M–3H]^2– charge state. The oligonucleotides with SNPs in the middle were also determined from the [M–2H]^2– precursor ion.

Keywords: single nucleotide polymorphisms (SNPs); high-performance liquid chromatography; electrospray ionization mass spectrometry; SNP site; retention order; charge state; product ion

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