Analysis of short tandem repeat polymorphisms by electrospray ion trap mass spectrometry

The application of electrospray ionization (ESI) ion trap mass spectrometry (MS) to the analysis of short tandem repeats (STRs or microsatellites) is described. Several equine dinucleotide STR loci were chosen as a model system to evaluate ESI ion trap as a routine instrument for rapid and reliable genoytping. With the use of specific primers STR loci were amplified from different blood samples having allele sizes between 60 and 100 bp. A new purification method based on reversible binding of PCR products to magnetic particles has proven to be directly compatible with ESI ion trap MS analysis. The sense and antisense strands of the PCR products with concentrations of ∼100 fmol/µl were measured with a mass accuracy of 0.01%. The simplicity of the purification method and the capability for automated handling together with the precise sizing of PCR products by ESI ion trap MS facilitate the large scale analysis of polymorphic STRs. Moreover, mixtures of different allele length as obtained for heterozygous samples could accurately be assigned as well as a C→G switch between the two strands of a PCR product.