title: SRMBuilder: a user-friendly tool for selected reaction monitoring data analysis.
abstract: 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.
authors.affiliation: Key Laboratory of Systems Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China. qhsheng@sibs.ac.cn
authors.forename: Quanhu
authors.initials: Q
authors.lastname: Sheng
authors.forename: Chaochao
authors.initials: C
authors.lastname: Wu
authors.forename: Zhiduan
authors.initials: Z
authors.lastname: Su
authors.forename: Rong
authors.initials: R
authors.lastname: Zeng
mesh_terms: D030562:Databases, Protein; D013058:Mass Spectrometry / Q000379:methods; D020543:Proteome / Q000032:analysis*; D040901:Proteomics / Q000379:methods*; D015203:Reproducibility of Results; D012984:Software; D013223:Statistics as Topic / Q000379:methods*
chemical_list: D020543:Proteome