Analysis of oligosaccharides and peptides using external source Fourier transform mass spectrometry

The analyses of oligosaccharides and peptides using an external source Fourier transform mass spectrometry (FTMS) instrument is described. The external source makes possible the combination of FTMS with low vacuum ionization sources for the analyses of non-volatile compounds. The advantages of FTMS can therefore be applied to biological molecules. Instrumental modifications required for the use of liquid secondary ion mass spectrometry (LSIMS) ionization are described.; The fragmentation reactions of oligosaccharides are investigated using model saccharides, isotopically labeled compounds, low-energy collisionally activated dissociation (CAD), and molecular orbital calculations. The effects of alkyl derivatives and charge state on the fragmentation behavior are determined. Mechanisms are proposed for glycosidic bond fragmentation and cross-ring cleavage reactions. The fragmentation behavior of saccharides during FTMS analysis and the utility of this technique for the development of a general method for their mass spectrometric analyses are discussed.; Peptide bond fragmentation reactions are investigated using FTMS with low-energy CAD. Tripeptides are used as model compounds in order to determine the important factors involved in cleavage of the peptide backbone. For tripeptides containing only neutral residues, there is a strong preference for cleavage of the C-terminal amide bond to form the b{dollar}sb2{dollar} ion. The behavior is postulated to be due to intramolecular proton transfer reactions which lead to charge-initiated fragmentation of the peptide bond. Proton transfer to form the b{dollar}sb2{dollar} precursor ion is predicted to have a low barrier relative to formation of the b{dollar}sb1{dollar} precursor ion. Using tandem mass spectrometry, the structure of the b{dollar}sb2{dollar} ion is determined to be a linear acylium ion. Analysis of peptides containing basic functional groups provided evidence for charge-initiated fragmentation reactions under low-energy CAD conditions.; The design and construction of a compact external source FTMS instrument is described. The instrument is designed to minimize cost by using smaller components and less pumping than previous designs. The performance of the instrument is evaluated using electron impact and LSIMS ionization. The potential of the instrument for the analysis of biological molecules is discussed.