Matrix-assisted laser desorption/ionization (MALDI) time-of-flight (TOF) mass spectrometry (MS) has developed over the past decade into a versatile tool for the analysis of nucleic acids and especially as a reliable genotyping platform. This chapter summarizes its use in the context of the most widely used MALDI-TOF MS genomics platform, the Sequenom MassARRAY system. MassARRAY genotyping is based upon region-specific PCR followed by allele-specific single base primer extension reactions which are then desalted, dispensed onto a silica array preloaded with matrix, and the genotyping products are resolved on the basis of mass using MALDI-TOF MS. The platform is versatile in that it can resolve multiplexed reactions (40+ separate loci per reaction), acquires and interprets data quickly, gives a quantitative output which reflects the amount of product generated for each allele within an assay for multiplexed reactions, and is highly sensitive. These characteristics coupled with integrated software for sequence annotation, assay design, data interpretation, and data storage have lead to its wide adoption and use for multiple nucleic acid analysis applications in both the realm of genomics research and molecular diagnostics.

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A molecular dynamic study has been undertaken on small acetonitrile clusters containing between two and nine molecules, with each molecule being treated as a rigid rotor. As a function of kinetic temperature, calculated dynamic quantities, such as the root mean square bond length fluctuation, show that the clusters exhibit distinct solidlike and liquidlike forms. Starting from ordered structures, very marked size differences are observed in the melting temperatures of the clusters, with odd-sized species being found to adopt a liquidlike state at temperatures ∼80 K below neighboring even-sized clusters. This phenomenon is attributed to a strong propensity for polar acetonitrile molecules to form stable antiparallel pairs. Thus, clusters of an odd size contain an unpaired molecule which becomes mobile at comparatively low temperatures. Power spectra calculated from velocity (translational and rotational) autocorrelation functions, show that rotational motion about the symmetry (C3) axis begins at temperatures significantly below the recognized melting points. In contrast, motion about each of the axes perpendicular to the symmetry axis remains hindered even in clusters that are liquidlike. Structure observed in the calculated power spectra for acetonitrile clusters at low temperatures, compares favorably with that seen in the bulk material from several different types of experiment. Such observations are assisted by the fact that the spectra are dominated by features attributable to stable molecular dimers. Qualitative support for some of the results reported here is to be found in recent experiments by Buck and co-workers [Ber. Bunsenges. Phys. Chem. 96, 1275 (1992)] on the photodissociation of small acetonitrile clusters. In particular, the latter show strong evidence of differences in behavior between odd- and even-sized clusters; it is suggested that the experiments could be sampling from a mixture of solidlike and liquidlike forms.