• Study of Protein Identification Algorithms and Ammonia Metabolism in Mosquitoes

      Wysocki, Vicki H.; Tan, Guanhong; Wysocki, Vicki H. (The University of Arizona., 2006)
      Two database search algorithms, SEQUEST and X!Tandem, were studied in detail. Research results showed that SEQUEST is relatively prone to identify single charged peptides, while X!Tandem is prone to identify highly charged peptides.Peptide fragmentation patterns associated with corresponding structure motifs are incorporated into SEQUEST Replica and X!Tandem Replica. Research results showed that selective cleavage rules for peptide fragmentation help improve peptide identification especially for selectively cleaved peptides. A tool that makes use of the peak intensity information in the experimental spectra is applied after a SEQUEST search to extract correct peptides. Results showed that more peptides could be correctly identified and a low false positive rate (<5%) was introduced by applying this tool after SEQUEST search.A new possible ammonia metabolic pathway in mosquitoes was proposed. Results showed that the major steps along this pathway were confirmed and the detailed transfer pathway of nitrogen was elucidated.