Selected Reaction Monitoring to Measure Proteins of Interest in Complex Samples: A Practical Guide
Biology and especially systems biology projects increasingly require the capability to detect and quantify specific sets of proteins across multiple samples, for example the components of a biological pathway through a set of perturbation-response experiments. Targeted proteomics based on selected reaction monitoring (SRM) has emerged as an ideal tool to this purpose, and complements the discovery capabilities of shotgun proteomics methods. SRM experiments rely on the development of specific, quantitative mass spectrometric assays for each protein of interest and their application to the quantification of the protein set in various biological samples. SRM measurements are multiplexed, namely, multiple proteins can be quantified simultaneously, and are characterized by a high reproducibility and a broad dynamic range. We provide here a practical guide to the development of SRM assays targeting a set of proteins of interest and to their application to complex biological samples.
Key wordsSelected reaction monitoring Targeted proteomics Protein quantitation Assay design Assay validation
We thank Paul J. Boersema and Martin Soste (ETH Zurich) for insightful discussions. We thank Brendan MacLean (University of Washington) for critical reading of the manuscript. P.P. is supported by an EU-FP7 ERC Starting Grant (FP7-ERC-StG-337965), by a FP7-Reintegration grant (FP7-PEOPLE-2010-RG-277147), by a Professorship grant from the Swiss National Science Foundation (grant PP00P3_133670), and by a Promedica Stiftung (grant 2-70669-11). Y.F. is supported by an ETH Research Grant (grant 4412-1).
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