肽质量指纹谱鉴定蛋白质时生物信息学分析条件的优化
发布时间：2019-01-06 12:56
【摘要】：为了优化肽质量指纹谱(peptide mass fingerprint,PMF)鉴定蛋白质的生物信息学分析条件。将牛碳酸酐酶2(carbonic anhydrase-2,CAH2)和人热休克蛋白70s(Hsp70s)进行2-DE分离、酶解,肽段经过MALDI-TOFMS分析得到PMF数据。选择Swissprot、MSDB、NCBInr、Random等数据库和MASCOT与MS-Fit搜索引擎,以牛CAH2为模型优化搜索参数,结果表明:Swissprot是适合做蛋白PMF分析的数据库;主要参数最佳设置为:漏切位点数为1个,肽质量容错数为±1Da,同时肽质量类型选择平均分子质量比单同位素质量更便于候选蛋白的筛选。最后用人Hsp70s蛋白的PMF数据检验优化条件,结果表明,所选择的数据库及参数是可靠的。
[Abstract]:In order to optimize the bioinformatics analysis conditions for protein identification by peptide mass fingerprint (peptide mass fingerprint,PMF). Bovine carbonic anhydrase 2 (carbonic anhydrase-2,CAH2) and human heat shock protein 70 s (Hsp70s) were separated by 2-DE and hydrolyzed. The PMF data were obtained by MALDI-TOFMS analysis. Swissprot,MSDB,NCBInr,Random database and MASCOT and MS-Fit search engine were selected to optimize the search parameters using bovine CAH2 as the model. The results showed that Swissprot was a suitable database for protein PMF analysis. The main parameters are as follows: the number of missing site is 1, the fault-tolerant number of peptide mass is 卤1Da. meanwhile, the selection of average molecular weight of peptide mass is more convenient than that of single isotope mass to screen candidate protein. Finally, the optimized conditions were tested with the PMF data of human Hsp70s protein. The results showed that the selected database and parameters were reliable.
【作者单位】： 重庆医科大学药学院药物分析教研室 重庆医科大学药学院生物化学与分子生物学教研室 重庆医科大学药学院药物分析教研室 重庆医科大学药学院药物分析教研室
【基金】：国家自然科学基金(No.30476021) 教育部博士点(No.教特发中心函【2004】166号)资助项目
【分类号】：Q51
，
本文编号：2402813
[Abstract]:In order to optimize the bioinformatics analysis conditions for protein identification by peptide mass fingerprint (peptide mass fingerprint,PMF). Bovine carbonic anhydrase 2 (carbonic anhydrase-2,CAH2) and human heat shock protein 70 s (Hsp70s) were separated by 2-DE and hydrolyzed. The PMF data were obtained by MALDI-TOFMS analysis. Swissprot,MSDB,NCBInr,Random database and MASCOT and MS-Fit search engine were selected to optimize the search parameters using bovine CAH2 as the model. The results showed that Swissprot was a suitable database for protein PMF analysis. The main parameters are as follows: the number of missing site is 1, the fault-tolerant number of peptide mass is 卤1Da. meanwhile, the selection of average molecular weight of peptide mass is more convenient than that of single isotope mass to screen candidate protein. Finally, the optimized conditions were tested with the PMF data of human Hsp70s protein. The results showed that the selected database and parameters were reliable.
【作者单位】： 重庆医科大学药学院药物分析教研室 重庆医科大学药学院生物化学与分子生物学教研室 重庆医科大学药学院药物分析教研室 重庆医科大学药学院药物分析教研室
【基金】：国家自然科学基金(No.30476021) 教育部博士点(No.教特发中心函【2004】166号)资助项目
【分类号】：Q51
，
本文编号：2402813
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