Nanomaterials play an increasingly important role in mass spectrometry, especially for selective analyte capture, delivery of sample to the mass spectrometer, and even as ionization matrices. We have an on-going Department of Energy/BES funded research project aimed at developing nanomaterials, specifically gold (Au) nanospheres and nanorods for: (i) LDI of model peptides using size-selected gold (Au) NP, investigations of the effects of trace amounts of chemical species (i.e., Na+, K+, NH4+, Cl-, PO43-, CO3-, and other frequently encountered ionic species present in biological buffer solutions) on the LDI process, (ii) the effects of ‘capping groups’ on LDI of peptides from AuNP. These studies clearly demonstrate that a properly designed nanoparticle can significantly enhance the ion yields as well as the range (molecular weight) of analytes. We have also shown that Au nanorods can be used to enhance ionization of peptides using extended wavelength lasers (1064 nm). Additionally, we are developing nanomatierals (spheres, rods, and conjugated forms of each) are for selective analyte capture and ionization using laser desorption ionization, and the potential of these new materials as matrices for molecular imaging of tissues and microarrays is currently being explored.