Analysis of Single Nucleotide Polymorphism Sites in Exon 4 of the p53 Gene Using High-Performance Liquid Chromatography/Electrospray Ionization/Tandem Mass Spectrometry

Three groups of four oligonucleotides with special single nucleotide polymorphism (SNP) sites in exon 4 of the p53 gene were analyzed with ion-pair, reversed-phase, high-performance liquid chromatography/electrospray ionization/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 tandem mass spectra of the oligonucleotides. SNPs at the 3′ end can easily be 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]³⁻, 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.