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Automated discrimination of polymerase chain reaction products with closely related sequences by software‐based detection of characteristic peaks in product ion spectra
Author(s) -
Muhammad Warees T.,
Tabb David L.,
Fox Karen F.,
Fox Alvin
Publication year - 2003
Publication title -
rapid communications in mass spectrometry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.528
H-Index - 136
eISSN - 1097-0231
pISSN - 0951-4198
DOI - 10.1002/rcm.1262
Subject(s) - chemistry , polymerase chain reaction , ion , product (mathematics) , nucleotide , spectral line , mass spectrum , polymerase , computational biology , analytical chemistry (journal) , dna , gene , chromatography , biochemistry , biology , physics , geometry , mathematics , organic chemistry , astronomy
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. Copyright © 2003 John Wiley & Sons, Ltd.