Tandem Mass Spectrometry Proteomics Data Processing New Method Of Process Improvement And Identification Of Glycosylation Of Peptides

The development of biomass related ionization method in 1988 and the accomplishment of human genome sequencing in 2001 are major breakthrough for Proteomic study. The key aspect of Proteomics is to identify complete information of the proteins in given sample. Different technology has been developed to achieve this goal. Among them, Shotgun is the most widely use technique.The principle of Shotgun technique is:after the extraction of proteins in the sample, using specific enzyme to digest proteins into peptides which suit the demands of mass spectrometry. LC-MS will be used for identification of peptides. Bioinformatic tools will be used to analyse the mass-spec data and report peptide & protein information. During this process, the complexity of proteins provides great challenge to data analysis.This article focus on the improvement of tandem-ms data analyse process and new method of glycopeptides identification. The main contents are:1)the improvement of tandem-ms data analyse process for LTQ; 2)improvement of database-search parameter for the identification of glycosylation site; 3)development of new glycopeptides identification method.The main contribution and innovation of this article are:1)thorough understanding of the limitation of existing tandem-ms data analyse process in our laboratory, offering an improved process and fully utilization of published software. Therefore, data quality has been greatly improved; 2) discovering the defect of existing database-search parameter for the identification of glycosylation site, offering a solution; 3) development of new software for glycopeptides identification. It is the first high-though intact-glycopeptide identification software at current stage. This software fully utilizes the peptide database derived from experiment, offering a new way of setting up a database in proteomic study.