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This is an abstract for a poster to be presented at the Fifth Foresight Conference on Molecular Nanotechnology. The full paper is now available.Determining the sequence of amino acids in proteins is an important step towards understanding the structure and function of proteins. Currently not all proteins are accessible for sequencing due to the limited availability of proteases, enzymes that cleave proteins at specific amino acids. Therefore a need for additional fragmentation methods exists. We are exploring the fragmentation of proteins with highly charged heavy ions (HCI), using ions extracted from the EBIT (electron beam ion trap) facility at Livermore. The ions carry charges of up to 65+ (Au, e.g.), which translate into potential energies comparable to the kinetic energies of a few 100 keV, stressing electronic interaction rather than collisional. In interaction studies with surfaces HCI have been found to extract up to a few 100 electrons per ion on approaching the surface. Oligopeptides deposited on a solid substrate were used as a target on which the ions were directed. Mass spectra of secondary ions ejected from the sample were obtained using a time-of-flight spectrometer. We have observed several processes, most notably the ejection of a series of distinctive molecular fragments, characteristic for each molecule. This indicates a specificity in the fragmentation processes, where cleavage occurs preferably at certain molecular sites. Intact molecule ejection also has been found to occur, as well as the attachment of alkali or halogenide ions to molecules. Besides fragmentation chemical alterations of the molecules are possible due to the removal of binding electrons. The occurrence of these processes is indicated by mass components exceeding the intact molecule mass in the spectra.