title: Automated discrimination of polymerase chain reaction products with closely related sequences by software-based detection of characteristic peaks in product ion spectra.
abstract: A computer-based method is described for automated detection of peaks in product ion spectra that allows discrimination of structurally related polymerase chain reaction (PCR) products. PCR products of K-ras mutants having single nucleotide substitutions and isomeric sequence changes in positions 1 and 2 of codon 12 (e.g. TGT and GTT) were used as a model system. SpecDiff, a tool for differentiating pairs of mass spectra by identifying peaks that either differ in relative intensity between spectra or only appear in one of a pair of spectra, was created to help automate detection. This program was demonstrated to have great utility in detection of mutations and could also be useful as a general tool for differentiating other molecules of closely related structure.
authors.affiliation: Department of Pathology and Microbiology, University of South Carolina School of Medicine, Columbia, SC 29209, USA.
authors.forename: Warees T
authors.initials: WT
authors.lastname: Muhammad
authors.forename: David L
authors.initials: DL
authors.lastname: Tabb
authors.forename: Karen F
authors.initials: KF
authors.lastname: Fox
authors.forename: Alvin
authors.initials: A
authors.lastname: Fox
mesh_terms: D000465:Algorithms; D001483:Base Sequence; D016000:Cluster Analysis; D003062:Codon / Q000032:analysis / Q000737:chemistry; D008969:Molecular Sequence Data; D009841:Oligonucleotides / Q000032:analysis* / Q000737:chemistry*; D010363:Pattern Recognition, Automated; D016133:Polymerase Chain Reaction / Q000379:methods*; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity; D016415:Sequence Alignment / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*; D021241:Spectrometry, Mass, Electrospray Ionization / Q000379:methods*
chemical_list: D003062:Codon; D009841:Oligonucleotides