Computational and experimental studies on positive ions derived from peptides

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Proteomics relies very heavily on mass spectrometry to determine the sequence of amino acids in at least a short segment of a protein. Usually the protein is broken down by an enzyme (trypsin) and the sequences of the amino acid residues in some of the product peptides are determined by their fragmentation in a mass spectrometry. The mechanisms by which peptides fragment are still not very well understood. We are addressing this problem in several ways. We are examining details of the mechanisms by which protonated peptides (the usual target) fragment; this frequently necessitates looking at the even simpler building blocks of peptides, the amino acids. We are also expanding fragmentation studies into two different classes of ions, (1) radical cations of peptides formed in electrospray mass spectrometry by breaking copper ion / peptide complexes, and (2) complexes of peptides attached to more highly charged ions like a La3+ ion. These two classes of ions will give different types of information about the peptides and will help clear up ambiguities in the sequencing information obtained from the protnated peptide studies. Throughout all this experimental work Density Functional Theory calculations will be used to determine the structures of intermediates and to determine the barriers to their interconversion.