The capability of tandem spectrometry to detect single and multiple SNPs in a single stretch of DNA will be evaluated. The p53 gene contains polymorphisms in codon 47 (TCG and CCG) and codon 47 (CGC and CCC). This will be studied as a model system. In initial work a 67 bp PCR product containing only the C to T switch will be analyzed by mass spectrometry (MS). In subsequent work 120 bp PCR products containing both alleles will be analyzed by MS2. This is pushing the envelope for mass discrimination using triple quadrupole or ion trap tandem mass spectrometry. The use of stable isotope labeled nucleotides increases the mass differences on C to T substitution (from 15 to 27 mass) units. This and the use of MSn (by sequential fragmentation of the molecule into smaller pieces) may be necessary to analyze larger PCR products.
