Automated discrimination of polymerase chain reaction products with closely related sequences by software-based detection of characteristic peaks in product ion spectra

Rapid Commun Mass Spectrom. 2003;17(24):2755-62. doi: 10.1002/rcm.1262.

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.

Publication types

  • Comparative Study
  • Evaluation Study
  • Research Support, U.S. Gov't, P.H.S.
  • Validation Study

MeSH terms

  • Algorithms*
  • Base Sequence
  • Cluster Analysis
  • Codon / analysis
  • Codon / chemistry
  • Molecular Sequence Data
  • Oligonucleotides / analysis*
  • Oligonucleotides / chemistry*
  • Pattern Recognition, Automated*
  • Polymerase Chain Reaction / methods*
  • Reproducibility of Results
  • Sensitivity and Specificity
  • Sequence Alignment / methods*
  • Sequence Analysis, DNA / methods*
  • Spectrometry, Mass, Electrospray Ionization / methods*

Substances

  • Codon
  • Oligonucleotides