Mining proteomic MS/MS data for MRM transitions.

Multiple reaction monitoring (MRM) of peptides is a popular proteomics technique that employs tandem mass spectrometry to quantify selected proteins of interest, such as those previously identified in differential protein identification studies. Using this technique, the specificity of precursor to product transitions is exploited to determine the absolute quantity of multiple proteins in a single sample. Selection of suitable transitions is critical for the success of MRM experiments, but accurate theoretical prediction of fragmentation patterns and peptide signal intensity is currently not possible. A recently proposed solution to this problem is to combine knowledge of the preferred properties of transitions for MRM, taken from expert practitioners, with MS/MS evidence extracted from a proteomics data repository. In addition, by predicting retention time for each peptide candidate, it allows selection of several compatible transition candidates that can be monitored simultaneously, permitting MRM. In this chapter, we explain how to go about designing transitions using the web-based transition design tool, MRMaid, which leverages high quality MS/MS evidence from the Genome Annotating Proteomic Pipeline (GAPP).