Computational approaches to selected reaction monitoring assay design

Abstract

Selected reaction monitoring (SRM) is becoming the tool of choice for targeted quantitative proteomics, with applications as diverse as clinical diagnostics and systems biology. Assay design is critical to the success of every SRM experiment. For each protein of interest it is necessary to find a set of peptides that can be monitored as surrogates for that protein. These peptides must satisfy a number of criteria, including uniqueness in the proteome, detectability by mass spectrometry, and suitability of product ion series. Finding peptides that meet all these criteria is time consuming, especially when seeking to quantify multiple proteins in a single run. In response to these challenges, a number of groups have developed freely available tools to assist in the process of SRM assay design - these include databases, online tools, and stand-alone software. This chapter introduces some of these tools and explains how they can help to facilitate reliable SRM experiments. © Springer Science+Business Media, LLC 2013.