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Selected reaction monitoring–based proteomics: workflows, potential, pitfalls and future directions

Abstract

Selected reaction monitoring (SRM) is a targeted mass spectrometry technique that is emerging in the field of proteomics as a complement to untargeted shotgun methods. SRM is particularly useful when predetermined sets of proteins, such as those constituting cellular networks or sets of candidate biomarkers, need to be measured across multiple samples in a consistent, reproducible and quantitatively precise manner. Here we describe how SRM is applied in proteomics, review recent advances, present selected applications and provide a perspective on the future of this powerful technology.

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Figure 1: The selected reaction monitoring technique.
Figure 2: Performance profiles of SRM-, affinity- and imaging-based methods to target protein quantification.
Figure 3: Examples of application of SRM in targeted proteomics.

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Acknowledgements

We thank R. Huettenhain for insightful discussions. P.P. is supported by a 'Foerderungsprofessur' grant from the Swiss National Science Foundation (grant PP00P3_133670) and by an EU Seventh Framework Program Reintegration grant (FP7-PEOPLE-2010-RG-277147), R.A. is supported by the European Research Council (grant ERC-2008-AdG 233226), SystemsX.ch, the Swiss initiative for systems biology (project PhosphonetX), by the EU Seventh Framework Program Proteomics Specification in Space and Time (PROSPECTS grant HEALTH-F4-2008) and by the Swiss National Science Foundation (grant 3100A0-130530).

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Correspondence to Paola Picotti.

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P.P. and R.A. are named as coinventors on a patent application (US2011178273, EP2124060, WO2009141141 and EP2283366) related to the generation of SRM assays and own shares of Biognosys, a spin-off company marketing products related to targeted proteomics.

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Picotti, P., Aebersold, R. Selected reaction monitoring–based proteomics: workflows, potential, pitfalls and future directions. Nat Methods 9, 555–566 (2012). https://doi.org/10.1038/nmeth.2015

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