Schematic view of quantitative and allele-specific expression analysis with real competitive PCR. A point mutation in the cDNA sequence is used as the marker for allele-specific gene expression analysis. The competitor is designed to have a synthetic mutation next to the natural mutation and is used for quantitative gene expression analysis. Three extension products from the two cDNA sequences and the competitor have different molecular weights, and are detected by MALDI-TOF MS. The peak area ratios of these products represent accurately the concentration ratios of the two cDNAs and the competitor. Since the absolute quantity of the competitor is known, the absolute quantities of the two cDNA sequences can be readily calculated.