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Nat Commun. 2016 Jan 12;7:8992. doi: 10.1038/ncomms9992.

A draft map of the mouse pluripotent stem cell spatial proteome.

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Department of Biochemistry, Cambridge Centre for Proteomics, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK.
Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK.
Department of Pharmacology, University of Pretoria, Arcadia 0007, Republic of South Africa.
Thermo Fisher Scientific, 355 River Oaks Pkwy, San Jose, California 95314, USA.


Knowledge of the subcellular distribution of proteins is vital for understanding cellular mechanisms. Capturing the subcellular proteome in a single experiment has proven challenging, with studies focusing on specific compartments or assigning proteins to subcellular niches with low resolution and/or accuracy. Here we introduce hyperLOPIT, a method that couples extensive fractionation, quantitative high-resolution accurate mass spectrometry with multivariate data analysis. We apply hyperLOPIT to a pluripotent stem cell population whose subcellular proteome has not been extensively studied. We provide localization data on over 5,000 proteins with unprecedented spatial resolution to reveal the organization of organelles, sub-organellar compartments, protein complexes, functional networks and steady-state dynamics of proteins and unexpected subcellular locations. The method paves the way for characterizing the impact of post-transcriptional and post-translational modification on protein location and studies involving proteome-level locational changes on cellular perturbation. An interactive open-source resource is presented that enables exploration of these data.

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