Optimization of bioinformatics analysis conditions by peptide mass fingerprint identify proteins

作者：Peng Yong Bo; Ma Yong Ping; Xia Yong Peng; Qiu Zong Yin^*

来源：Chinese Journal of Analytical Chemistry, 2008, 36(4): 467-472.

• matrix assisted laser desorption ionization-time-of flight-mass spectrometry
• peptide mass fingerprint search
• protein

The study aim was to optimize the bioinformatics analysis conditions (databases and major parameters) in process of Peptide Mass Fingerprint (PMF) identify target proteins. In this process of experiment design and analysis, the Bovine Carbonic anhydrase-2 (CAH2_BOVIN) and human Hsp70s protein (Heat shock protein 70) were separate by 2-DE, proteolysis by trypsin gold, then the lysised peptides were gathered and analyzed using MALDI-TOF MS and the peptides mass data and mass spectra were obtained. In this study, Swissprot, MSDB, NCBInr, Random databases, MASCOT and MS-Fit were selected as search engines, the standard CAH2_BOVIN used as model to set up protein search standard conditions. Results show that Swissprot is the better database for proteins PMF study, and the better missed cleavage is one site and the better peptide tolerance is 1 Da, average peptide mass type better than monoisotopic type to get target proteins.. Then human Hsp70s protein mass data were used as sample to check the accuracy of MS search standard conditions. Results show that the optimized databases and parameters are reliable.

• 出版日期2008-4
• 单位重庆医科大学