This article is part of the supplement: Statistical mass spectrometry-based proteomics
In silico design of targeted SRM-based experiments
Center for Bioinformatics, Quantitative Biology Center, and Department of Computer Science, University of Tübingen, Germany
BMC Bioinformatics 2012, 13(Suppl 16):S8 doi:10.1186/1471-2105-13-S16-S8Published: 5 November 2012
Selected reaction monitoring (SRM)-based proteomics approaches enable highly sensitive and reproducible assays for profiling of thousands of peptides in one experiment. The development of such assays involves the determination of retention time, detectability and fragmentation properties of peptides, followed by an optimal selection of transitions. If those properties have to be identified experimentally, the assay development becomes a time-consuming task. We introduce a computational framework for the optimal selection of transitions for a given set of proteins based on their sequence information alone or in conjunction with already existing transition databases. The presented method enables the rapid and fully automated initial development of assays for targeted proteomics. We introduce the relevant methods, report and discuss a step-wise and generic protocol and we also show that we can reach an ad hoc coverage of 80 % of the targeted proteins. The presented algorithmic procedure is implemented in the open-source software package OpenMS/TOPP.