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Localisation of proteins within subcellular niches is a fundamental mechanism for the post-translational regulation of protein function. The high throughput and flexibility of quantitative mass spectrometry make it a highly complementary approach to the microscopy techniques typically used for such studies, although robust performance is dependent on accurate and precise quantification. In this chapter we review several proteomics methods that have been devised for this purpose, utilising label-free quantification, in vivo metabolic labelling, and isobaric tagging, and consider the strengths and limitations of their implementation.

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