Structures and stabilities of small gas-phase ions

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This project involves fundamental chemistry of peptides. Peptides are small molecules composed of amino acids, the building blocks of proteins. How amino acids are combined defines the structure of a protein and its biological function. We determine the sequence of amino acids using an enzyme to break the protein into peptides. I study the structures of protonated peptides and how they break apart in a mass spectrometer. Amino acid residues are usually lost from one end of a protonated peptide. This makes it possible to identify a peptide (and hence the protein from which it was derived) from the fragments formed. Problems arise when linear intermediate ions rearrange via cyclic ions and then reopen to different linear ions. This leads to incorrect sequence information. In this proposal, I will examine the structures of unusual ions formed in the fragmentation of protonated peptides using a combination of mass spectrometry, molecular modeling and infrared spectroscopy. Theory will provide insights into mechanisms by which these ions fragment and/or rearrange.