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Temporally controlled stable-isotope labelling in vivo, coupled with accurate and sensitive mass spectrometry has the potential to reveal the complexity of protein turnover at the level of the proteome. At present, there have been relatively few studies that are distributed across a broad range of experimental systems and analytical strategies, and no optimal workflows or analytical solutions have emerged. In this chapter we explore many of the considerations that need to be resolved in a well-designed workflow, and address the computational strategies that are needed after the data acquisition phase. We conclude that turnover studies are maturing and are experimentally within reach but that downstream software for analysis of turnover data is still in early stages of development.

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