Effective enrichment and mass spectrometry analysis of phosphopeptides using mesoporous metal oxide nanomaterials.

Mass spectrometry (MS)-based phosphoproteomics remains challenging due to the low abundance of phosphoproteins and substoichiometric phosphorylation. This demands better methods to effectively enrich phosphoproteins/peptides prior to MS analysis. We have previously communicated the first use of mesoporous zirconium dioxide (ZrO(2)) nanomaterials for effective phosphopeptide enrichment. Here, we present the full report including the synthesis, characterization, and application of mesoporous titanium dioxide (TiO(2)), ZrO(2), and hafnium dioxide (HfO(2)) in phosphopeptide enrichment and MS analysis. Mesoporous ZrO(2) and HfO(2) are demonstrated to be superior to TiO(2) for phosphopeptide enrichment from a complex mixture with high specificity (>99%), which could almost be considered as a "purification", mainly because of the extremely large active surface area of mesoporous nanomaterials. A single enrichment and Fourier transform MS analysis of phosphopeptides digested from a complex mixture containing 7% of alpha-casein identified 21 out of 22 phosphorylation sites for alpha-casein. Moreover, the mesoporous ZrO(2) and HfO(2) can be reused after a simple solution regeneration procedure with comparable enrichment performance to that of fresh materials. Mesoporous ZrO(2) and HfO(2) nanomaterials hold great promise for applications in MS-based phosphoproteomics.

RNA-templated semiconductor nanocrystals.

The use of a biomolecular RNA template for the synthesis of CdS semiconductor nanocrystals is described. Transfer RNA, with a well-defined three-dimensional structure, is used as a scaffold and ligand system in the aqueous synthesis of CdS. We have found that nanocrystal structures can be modulated by the structure of the templating tRNA. When possessing a folded three-dimensional structure, tRNA-templated synthesis yields a single product. If the same tRNA is rendered unstructured through the introduction of destabilizing mutations, a range of products are observed. The results reported indicate that biomolecules can be used to systematically engineer the structures and properties of semiconductor-based materials, and that the synergy between the dimensions of nanostructures and biomolecules provides a means to tune the properties of materials with nanoscale precision.

Nucleotide-directed growth of semiconductor nanocrystals.

We engineer colloidal quantum dot nanocrystals through the choice of biomolecular ligands responsible for nanoparticle nucleation, growth, stabilization, and passivation. We systematically vary the presence of, and thereby elucidate the role of, phosphate groups and a multiplicity of functionalities on the mononucleotides used as ligands. The results provide the basis for synthesis of nanoparticles using precisely controlled synthetic oligonucleotide sequences.