Cavities on a proteins surface as well as specific amino acid positioning within it create the physicochemical properties needed for a protein to perform its function. CASTp () is an online tool that locates and measures pockets and voids on 3D protein structures. This new version of CASTp includes annotated functional information of specific residues on the protein structure. The annotations are derived from the Protein Data Bank (PDB), Swiss-Prot, as well as Online Mendelian Inheritance in Man (OMIM), the latter contains information on the variant single nucleotide polymorphisms (SNPs) that are known to cause disease. These annotated residues are mapped to surface pockets, interior voids or other regions of the PDB structures. We use a semi-global pair-wise sequence alignment method to obtain sequence mapping between entries in Swiss-Prot, OMIM and entries in PDB. The updated CASTp web server can be used to study surface features, functional regions and specific roles of key residues of proteins.

A recent innovation in mass spectrometry is the ability to record mass spectra on ordinary samples, in their native environment, without sample preparation or preseparation by creating ions outside the instrument. In desorption electrospray ionization (DESI), the principal method described here, electrically charged droplets are directed at the ambient object of interest; they release ions from the surface, which are then vacuumed through the air into a conventional mass spectrometer. Extremely rapid analysis is coupled with high sensitivity and high chemical specificity. These characteristics are advantageously applied to high-throughput metabolomics, explosives detection, natural products discovery, and biological tissue imaging, among other applications. Future possible uses of DESI for in vivo clinical analysis and its adaptation to portable mass spectrometers are described.

A low-temperature plasma (LTP) probe has been developed for ambient desorption ionization. An ac electric field is used to induce a dielectric barrier discharge through use of a specially designed electrode configuration. The low-temperature plasma is extracted from the probe where it interacts directly with the sample being analyzed, desorbing and ionizing surface molecules in the ambient environment. This allows experiments to be performed without damage to the sample or underlying substrate and, in the case of biological analysis on skin surfaces, without electrical shock or perceptible heating. Positive or negative ions are produced from a wide range of chemical compounds in the pure stateand as mixtures in the gaseous, solution, or condensed phases, using He, Ar, N2, or ambient air as the discharge gas. Limited fragmentation occurs, although it is greater in the cases of the molecular than the atomic discharge gases. The effectiveness of the LTP probe has been demonstrated by recording characteristic mass spectra and tandem mass spectra of samples containing hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) and 2,4,6-trinitrotoluene (TNT) from poly(tetrafluoroethylene) (PTFE) surfaces where limits of detection are as low as 5 pg. Other performance characteristics, when using a commercial ion trap mass spectrometer, include 3-4 orders of magnitude linear dynamic range in favorable cases. Demonstration applications include direct analysis of cocaine from human skin, determination of active ingredients directly in drug tablets, and analysis of toxic and therapeutic compounds in complex biological samples. Ionization of chemicals directly from bulk aqueous solution has been demonstrated, where limits of detection are as low as 1 ppb. Large surface area sampling and control of fragmentation by a simple adjustment of the electrode configuration during operation are other demonstrated characteristics of the method.