Allelic loss analysis by denaturing high-performance liquid chromatography and electrospray ionization mass spectrometry

Frontiers of mass spectrometry in nucleic acids analysis

Nucleic acids research is a highly competitive field of research. A number of well established methods are available. The current output of high throughput ("next generation") sequencing technologies is impressive, and still technologies are continuing to make progress regarding read lengths, bp per second, accuracy and costs. Although in the 1990s MS was considered as an analytical platform for sequencing, it was soon realized that MS will never be competitive. Thus, the focus shifted from de novo sequencing towards other areas of application where MS has proven to be a powerful analytical tool. Potential niches for the application of MS in nucleic acids research include genotyping of genetic markers (single nucleotide polymorphisms, short tandem repeats, and combinations thereof), quality control of synthetic oligonucleotides, metabolic profiling of therapeutics, characterization of modified nucleobases in DNA and RNA molecules, and the study of non covalent interactions among nucleic acids as well as interactions of nucleic acids with drugs and proteins. The diversity of possible applications for MS highlights its significance for nucleic acid research.

Forensic DNA fingerprinting by liquid chromatography-electrospray ionization mass spectrometry

The determination of the molecular mass of a DNA sequence has several benefits over conventional fragment-length analysis that are advantageous to the forensic field: (i) sequence variation is captured that increases the power of discrimination compared with that obtained by conventional fragment-length analysis. First experiments showed that this increase makes up to 20%-30% for STR analysis. The new technical approach does not invalidate established developments and data, but adds to this information with additional discriminative categories. (ii) ICEMS is faster and cheaper than electrophoresis, does not require internal size standards, allelic ladders, or spectral calibration, which are necessary for fluorescence-based electrophoresis. (iii) ICEMS can unequivocally detect any single sequence variation in DNA molecules with lengths up to 250 nucleotides. This allows for maximum discrimination of forensically relevant DNA fragments, covering all sorts of STRs, SNPs, and also the analysis of the hypervariable segments of mtDNA. More effort, however, needs to be put into software development that escorts the analysis and data interpretation processes to make this technology manageable for the practical user.