| In chapter one, performic oxidation was explored as a method for sample pretreatment in proteomics. In addition to well-known modifications such as oxidation of tryptophan and oxidation and chlorination of tyrosine, novel degradation products including nonspecific cleavage after asparagine or tryptophan, formylation of lysine, and β-elimination of cysteine, were observed. The extreme complexity of sample and uninformative fragmentation of peptides in MS/MS experiments were two of the challenges faced by proteomics. A strategy based on performic oxidation and aimed at tackling these two problems was presented. Briefly, proteins were first oxidized by performic acid and then hydrolyzed by trypsin. The resulted sulfonic peptides were enriched by SCX HPLC exploited the negative solution charge of sulfonic group. The sulfonic peptide could be easily detected in negative MALDI-MS mode and showed both enhanced fragmentation efficiency and a simplified spectrum in positive MALDI-MS/MS experiment. The strength of the strategy was demonstrated by applying to bovine serum albumin. Potential use of the strategy in proteomics was also discussed.The covalent attachment of carbohydrate chains is a ubiquitous co- and post-translational protein modifications which frequently modulates the structures and functions of proteins. In despite of its importance, deciphering glycosylation of proteins is still an unsolved problem in proteome research. In chapter two, the quantity of glyans and sialic acids as well as glycosylated sites in recombinant glycoproteins, i.e. human pro-urokinase and platelet-derived growth factor-BB, were determined using biological mass spectrometry. The data obtained provide valuable parameters for quality control of this kind of drugs. The experience obtained also constituted a good preparation for subsequent glycosylation analysis at the proteomics level.
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