Large-scale genotyping by mass spectrometry: experience, advances and obstacles

Single nucleotide polymorphism (SNP) genotyping has become a key technology for genetic studies. In recent years, matrix-assisted laser desorption/ionization (MALDI) time-of-flight mass spectrometry has emerged as a very powerful method for SNP genotyping. Here, we discuss our experience in implementing a high-throughput SNP genotyping facility based on MALDI, and the issues encountered in adapting this to large-scale genetic studies. Most of these issues are not specific to using MALDI approaches, and they will also serve as valuable pointers for establishing high-throughput genotyping with other methods.