ANALYSIS OF DNA FRAGMENTS FROM CONVENTIONAL AND MICROFABRICATED PCR DEVICES USING DELAYED EXTRACTION MALDI-TOF MASS-SPECTROMETRY

Applications of polymerase chain reaction (PCR) product analysis using rapid affinity capture followed by delayed extraction (DE) MALDI-TOFM S is presented. Such applications include multiplex short tandem repea t (STR) typing, which is demonstrated for STR systems from conventiona l and microchip-based thermal cycling instruments. Using the combinati on of the microfabricated PCR instrument and DE-MALDI-TOFMS, a complet e genotyping assay can be performed in under 50 min with a resultant m olecular weight accuracy approaching or exceeding 100 ppm through exte rnal calibration. The observed resolution and mass accuracy for a 69-b ase PCR product enables identification of single base substitutions by direct molecular weight determination.