Sheng Quanhu, Wu Chaochao, Su Zhiduan, Zeng Rong
Key Laboratory of Systems Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.
J Bioinform Comput Biol. 2011 Dec;9 Suppl 1:51-62. doi: 10.1142/s0219720011005756.
With high sensitivity and reproducibility, selected reaction monitoring (SRM) has become increasingly popular in proteome research for targeted quantification of low abundance proteins and post translational modification. SRM is also well accepted in other mass-spectrometry based research areas such as lipidomics and metabolomics, which necessitates the development of easy-to-use software for both post-acquisition SRM data analysis and quantification result validation. Here, we introduce a software tool SRMBuilder, which can automatically parse SRM data in multiple file formats, assign transitions to compounds, match light/heavy transition/compound pairs and provide a user-friendly graphic interface to manually validate the quantification result at transition/compound/sample level. SRMBuilder will greatly facilitate processing of the post-acquisition data files and validation of quantification result for SRM. The software can be downloaded for free from http://www.proteomics.ac.cn/software/proteomicstools/index.htm as part of the software suite ProteomicsTools.
选择反应监测（SRM）具有高灵敏度和可重复性，在蛋白质组研究中越来越受欢迎，用于低丰度蛋白质的靶向定量和翻译后修饰。SRM在其他基于质谱的研究领域如脂质组学和代谢组学中也得到了广泛认可，这就需要开发易于使用的软件，用于采集后SRM数据分析和定量结果验证。在此，我们介绍一款软件工具SRMBuilder，它可以自动解析多种文件格式的SRM数据，为化合物分配跃迁，匹配轻/重跃迁/化合物对，并提供用户友好的图形界面，以便在跃迁/化合物/样品水平上手动验证定量结果。SRMBuilder将极大地促进采集后数据文件的处理以及SRM定量结果的验证。该软件可作为ProteomicsTools软件套件的一部分从http://www.proteomics.ac.cn/software/proteomicstools/index.htm免费下载。
